8YNQ

ATP-grasp peptide ligase from Streptomyces

PDB DOI: https://doi.org/10.2210/pdb8YNQ/pdb

Classification: LIGASE
Organism(s): Streptomyces albogriseolus 1-36
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-03-11 Released: 2025-02-19
Deposition Author(s): Xu, M.J., Yan, Y.Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 ?
R-Value Free:
0.319 (Depositor), 0.327 (DCC)
R-Value Work:
0.234 (Depositor), 0.247 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of ATP-grasp peptide ligase at 2.2 Angstroms resolution.

Xu, M.J., Yan, Y.Q.

To be published.

Macromolecule Content

Total Structure Weight: 200.19 kDa
Atom Count: 13,135
Modelled Residue Count: 1,635
Deposited Residue Count: 1,792
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-grasp peptide ligase	A [auth C], B [auth D], C [auth A], D [auth B]	448	Streptomyces albogriseolus 1-36	Mutation(s): 0 Gene Names: Alb28
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain I [auth C] MOL2 format, chain E [auth C] MOL2 format, chain I [auth C] mmCIF format, chain E [auth C] mmCIF format, chain I [auth C]	E [auth C], I [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain E [auth C] Focus chain I [auth C] Interactions & Density Focus chain E [auth C] Focus chain I [auth C]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
TRS (Subject of Investigation/LOI) Query on TRS Download Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B] mmCIF format, chain X [auth B]	X [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain L [auth D] SDF format, chain N [auth D] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain H [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain H [auth C] mmCIF format, chain L [auth D] mmCIF format, chain N [auth D] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	H [auth C] L [auth D] N [auth D] P [auth A] Q [auth A] H [auth C], L [auth D], N [auth D], P [auth A], Q [auth A], R [auth A], S [auth A], U [auth B], V [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain L [auth D] Focus chain N [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain H [auth C] Focus chain L [auth D] Focus chain N [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain V [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain T [auth A] SDF format, chain W [auth B] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain T [auth A] MOL2 format, chain W [auth B] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain T [auth A] mmCIF format, chain W [auth B]	F [auth C] G [auth C] J [auth D] K [auth D] T [auth A] F [auth C], G [auth C], J [auth D], K [auth D], T [auth A], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Focus chain G [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain T [auth A] Focus chain W [auth B] Interactions & Density Focus chain F [auth C] Focus chain G [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain T [auth A] Focus chain W [auth B]