9H8P

Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, mutant DTT

PDB DOI: https://doi.org/10.2210/pdb9H8P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodococcus jostii RHA1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-10-29 Released: 2025-01-29
Deposition Author(s): Rozeboom, H.J., Fraaije, M.W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 ?
R-Value Free:
0.165 (Depositor), 0.165 (DCC)
R-Value Work:
0.149 (Depositor), 0.149 (DCC)
R-Value Observed:
0.150 (Depositor)

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

Biocatalytic Cleavage of para-Acetoxy Benzyl Ethers: Application to Protecting Group Chemistry

Ashley, B., Demingo, C., Rozeboom, H., Bianciardi, N., Dunleavy, T., Haaksma, J.J., Guo, Y., Fraaije, M.W.

(2025) ACS Catal 15: 105-113

DOI: https://doi.org/10.1021/acscatal.4c04257

Macromolecule Content

Total Structure Weight: 480.33 kDa
Atom Count: 36,894
Modelled Residue Count: 4,200
Deposited Residue Count: 4,208
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable vanillyl-alcohol oxidase	A, B, C, D, E A, B, C, D, E, F, G, H	526	Rhodococcus jostii RHA1	Mutation(s): 8 Gene Names: RHA1_ro03282 EC: 1.1.3.38
UniProt
Find proteins for Q0SBK1 (Rhodococcus jostii (strain RHA1)) Explore Q0SBK1 Go to UniProtKB: Q0SBK1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0SBK1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain HA [auth G] SDF format, chain I [auth A] SDF format, chain JA [auth H] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E]	DA [auth F] HA [auth G] I [auth A] JA [auth H] O [auth B] DA [auth F], HA [auth G], I [auth A], JA [auth H], O [auth B], S [auth C], V [auth D], Z [auth E]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain DA [auth F] Focus chain HA [auth G] Focus chain I [auth A] Focus chain JA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain DA [auth F] Focus chain HA [auth G] Focus chain I [auth A] Focus chain JA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Z [auth E]
B3P Query on B3P Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain EA [auth F] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth H] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	AA [auth E] EA [auth F] J [auth A] K [auth A] KA [auth H] AA [auth E], EA [auth F], J [auth A], K [auth A], KA [auth H], P [auth B], T [auth C], Y [auth D]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth H] Focus chain P [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth H] Focus chain P [auth B] Focus chain T [auth C] Focus chain Y [auth D]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain L [auth A] SDF format, chain Q [auth B] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B]	BA [auth E], FA [auth F], L [auth A], Q [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain BA [auth E] Focus chain FA [auth F] Focus chain L [auth A] Focus chain Q [auth B] Interactions & Density Focus chain BA [auth E] Focus chain FA [auth F] Focus chain L [auth A] Focus chain Q [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain GA [auth F] SDF format, chain IA [auth G] SDF format, chain LA [auth H] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	CA [auth E] GA [auth F] IA [auth G] LA [auth H] N [auth A] CA [auth E], GA [auth F], IA [auth G], LA [auth H], N [auth A], R [auth B], U [auth C], W [auth D], X [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain N [auth A] Focus chain R [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain N [auth A] Focus chain R [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D]