8R3A | pdb_00008r3a

NT-26 Arsenite oxidase B F108C-G123C

PDB DOI: https://doi.org/10.2210/pdb8R3A/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudorhizobium banfieldiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-11-08 Released: 2025-05-21
Deposition Author(s): Engrola, F., Santos-Silva, T., Correia, M.A.S., Romao, M.J.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 ?
R-Value Free:
0.185 (Depositor), 0.185 (DCC)
R-Value Work:
0.152 (Depositor), 0.152 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

NT-26 Arsenite oxidase B F108C-G123C

Engrola, F., Santos-Silva, T.

To be published.

Macromolecule Content

Total Structure Weight: 460.34 kDa
Atom Count: 34,000
Modeled Residue Count: 3,903
Deposited Residue Count: 4,080
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AroA	A, C, E, G	845	Pseudorhizobium banfieldiae	Mutation(s): 0 Gene Names: aroA EC: 1.20.98.1
UniProt
Find proteins for Q6VAL8 (Pseudorhizobium banfieldiae) Explore Q6VAL8 Go to UniProtKB: Q6VAL8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6VAL8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster	B, D, F, H	175	Pseudorhizobium banfieldiae	Mutation(s): 2 Gene Names: aioB EC: 1.20.98.1
UniProt
Find proteins for L0NMC5 (Pseudorhizobium banfieldiae) Explore L0NMC5 Go to UniProtKB: L0NMC5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L0NMC5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD (Subject of Investigation/LOI) Query on MGD Download Ideal Coordinates CCD File SDF format, chain FB [auth E] SDF format, chain GB [auth E] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain VB [auth G] SDF format, chain WB [auth G] MOL2 format, chain FB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain VB [auth G] MOL2 format, chain WB [auth G] mmCIF format, chain FB [auth E] mmCIF format, chain GB [auth E] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain VB [auth G] mmCIF format, chain WB [auth G]	FB [auth E] GB [auth E] HA [auth C] IA [auth C] S [auth A] FB [auth E], GB [auth E], HA [auth C], IA [auth C], S [auth A], T [auth A], VB [auth G], WB [auth G]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ VQAGYJCYOLHZDH-ILXWUORBSA-N		Interactions Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain S [auth A] Focus chain T [auth A] Focus chain VB [auth G] Focus chain WB [auth G] Interactions & Density Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain S [auth A] Focus chain T [auth A] Focus chain VB [auth G] Focus chain WB [auth G]
P33 Query on P33 Download Ideal Coordinates CCD File SDF format, chain HB [auth E] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain V [auth A] SDF format, chain XB [auth G] MOL2 format, chain HB [auth E] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain XB [auth G] mmCIF format, chain HB [auth E] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain XB [auth G]	HB [auth E], KA [auth C], LA [auth C], V [auth A], XB [auth G]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain HB [auth E] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain V [auth A] Focus chain XB [auth G] Interactions & Density Focus chain HB [auth E] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain V [auth A] Focus chain XB [auth G]
F3S (Subject of Investigation/LOI) Query on F3S Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain K [auth A] SDF format, chain MB [auth G] SDF format, chain PA [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain MB [auth G] MOL2 format, chain PA [auth E] mmCIF format, chain BA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain MB [auth G] mmCIF format, chain PA [auth E]	BA [auth C], K [auth A], MB [auth G], PA [auth E]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain K [auth A] Focus chain MB [auth G] Focus chain PA [auth E] Interactions & Density Focus chain BA [auth C] Focus chain K [auth A] Focus chain MB [auth G] Focus chain PA [auth E]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain EB [auth E] MOL2 format, chain EB [auth E] mmCIF format, chain EB [auth E]	EB [auth E]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain EB [auth E] Interactions & Density Focus chain EB [auth E]
FES (Subject of Investigation/LOI) Query on FES Download Ideal Coordinates CCD File SDF format, chain AC [auth H] SDF format, chain KB [auth F] SDF format, chain NA [auth D] SDF format, chain Z [auth B] MOL2 format, chain AC [auth H] MOL2 format, chain KB [auth F] MOL2 format, chain NA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain AC [auth H] mmCIF format, chain KB [auth F] mmCIF format, chain NA [auth D] mmCIF format, chain Z [auth B]	AC [auth H], KB [auth F], NA [auth D], Z [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain AC [auth H] Focus chain KB [auth F] Focus chain NA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain AC [auth H] Focus chain KB [auth F] Focus chain NA [auth D] Focus chain Z [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain CB [auth E] SDF format, chain DB [auth E] SDF format, chain EA [auth C] SDF format, chain M [auth A] SDF format, chain OB [auth G] SDF format, chain QB [auth G] SDF format, chain R [auth A] SDF format, chain RA [auth E] SDF format, chain SA [auth E] SDF format, chain VA [auth E] SDF format, chain WA [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain EA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain OB [auth G] MOL2 format, chain QB [auth G] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] mmCIF format, chain CB [auth E] mmCIF format, chain DB [auth E] mmCIF format, chain EA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain OB [auth G] mmCIF format, chain QB [auth G] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth E] mmCIF format, chain SA [auth E] mmCIF format, chain VA [auth E] mmCIF format, chain WA [auth E]	CB [auth E] DB [auth E] EA [auth C] M [auth A] OB [auth G] CB [auth E], DB [auth E], EA [auth C], M [auth A], OB [auth G], QB [auth G], R [auth A], RA [auth E], SA [auth E], VA [auth E], WA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EA [auth C] Focus chain M [auth A] Focus chain OB [auth G] Focus chain QB [auth G] Focus chain R [auth A] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain VA [auth E] Focus chain WA [auth E] Interactions & Density Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EA [auth C] Focus chain M [auth A] Focus chain OB [auth G] Focus chain QB [auth G] Focus chain R [auth A] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain VA [auth E] Focus chain WA [auth E]
SER Query on SER Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain JA [auth C] SDF format, chain U [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain U [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain U [auth A]	JA [auth C], U [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain JA [auth C] Focus chain U [auth A] Interactions & Density Focus chain JA [auth C] Focus chain U [auth A]
4MO (Subject of Investigation/LOI) Query on 4MO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain J [auth A] SDF format, chain LB [auth G] SDF format, chain OA [auth E] MOL2 format, chain AA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain LB [auth G] MOL2 format, chain OA [auth E] mmCIF format, chain AA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain LB [auth G] mmCIF format, chain OA [auth E]	AA [auth C], J [auth A], LB [auth G], OA [auth E]	MOLYBDENUM(IV) ION Mo ZIKKVZAYJJZBGE-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain J [auth A] Focus chain LB [auth G] Focus chain OA [auth E] Interactions & Density Focus chain AA [auth C] Focus chain J [auth A] Focus chain LB [auth G] Focus chain OA [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain IB [auth E] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain YB [auth G] MOL2 format, chain IB [auth E] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain YB [auth G] mmCIF format, chain IB [auth E] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain YB [auth G]	IB [auth E], W [auth A], X [auth A], YB [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IB [auth E] Focus chain W [auth A] Focus chain X [auth A] Focus chain YB [auth G] Interactions & Density Focus chain IB [auth E] Focus chain W [auth A] Focus chain X [auth A] Focus chain YB [auth G]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain BC [auth H] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain NB [auth G] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PB [auth G] SDF format, chain Q [auth A] SDF format, chain QA [auth E] SDF format, chain RB [auth G] SDF format, chain SB [auth G] SDF format, chain TA [auth E] SDF format, chain TB [auth G] SDF format, chain UA [auth E] SDF format, chain UB [auth G] SDF format, chain XA [auth E] SDF format, chain YA [auth E] SDF format, chain ZA [auth E] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain BC [auth H] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth G] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain RB [auth G] MOL2 format, chain SB [auth G] MOL2 format, chain TA [auth E] MOL2 format, chain TB [auth G] MOL2 format, chain UA [auth E] MOL2 format, chain UB [auth G] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain ZA [auth E] mmCIF format, chain AB [auth E] mmCIF format, chain BB [auth E] mmCIF format, chain BC [auth H] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth G] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain RB [auth G] mmCIF format, chain SB [auth G] mmCIF format, chain TA [auth E] mmCIF format, chain TB [auth G] mmCIF format, chain UA [auth E] mmCIF format, chain UB [auth G] mmCIF format, chain XA [auth E] mmCIF format, chain YA [auth E] mmCIF format, chain ZA [auth E]	AB [auth E] BB [auth E] BC [auth H] CA [auth C] DA [auth C] AB [auth E], BB [auth E], BC [auth H], CA [auth C], DA [auth C], FA [auth C], GA [auth C], L [auth A], N [auth A], NB [auth G], O [auth A], P [auth A], PB [auth G], Q [auth A], QA [auth E], RB [auth G], SB [auth G], TA [auth E], TB [auth G], UA [auth E], UB [auth G], XA [auth E], YA [auth E], ZA [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain BC [auth H] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain L [auth A] Focus chain N [auth A] Focus chain NB [auth G] Focus chain O [auth A] Focus chain P [auth A] Focus chain PB [auth G] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain RB [auth G] Focus chain SB [auth G] Focus chain TA [auth E] Focus chain TB [auth G] Focus chain UA [auth E] Focus chain UB [auth G] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain BC [auth H] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain L [auth A] Focus chain N [auth A] Focus chain NB [auth G] Focus chain O [auth A] Focus chain P [auth A] Focus chain PB [auth G] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain RB [auth G] Focus chain SB [auth G] Focus chain TA [auth E] Focus chain TB [auth G] Focus chain UA [auth E] Focus chain UB [auth G] Focus chain XA [auth E] Focus chain YA [auth E] Focus chain ZA [auth E]
O (Subject of Investigation/LOI) Query on O Download Ideal Coordinates CCD File SDF format, chain JB [auth E] SDF format, chain MA [auth C] SDF format, chain Y [auth A] SDF format, chain ZB [auth G] MOL2 format, chain JB [auth E] MOL2 format, chain MA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain ZB [auth G] mmCIF format, chain JB [auth E] mmCIF format, chain MA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain ZB [auth G]	JB [auth E], MA [auth C], Y [auth A], ZB [auth G]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain JB [auth E] Focus chain MA [auth C] Focus chain Y [auth A] Focus chain ZB [auth G] Interactions & Density Focus chain JB [auth E] Focus chain MA [auth C] Focus chain Y [auth A] Focus chain ZB [auth G]