8YNQ | pdb_00008ynq

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 Å
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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural Insights into the Substrate Recognition Mechanism of an ATP-Grasp Peptide-Ligase Producing Diverse Dipeptides Containing Unnatural Amino Acids

Yan, Y.Q., Li, S.Y., Wu, X.N., Zhou, T., Li, J.X., Huang, S.X., Zheng, J.T., Xu, J., Da, L.T., Xu, M.J.

(2025) ACS Catal 15: 2550-2560

DOI: https://doi.org/10.1021/acscatal.4c07750

Macromolecule Content

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

Macromolecules

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| 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
UniProt
Find proteins for A0ACD6BA05 (Streptomyces sp. SID14515) Explore A0ACD6BA05 Go to UniProtKB: A0ACD6BA05
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6BA05
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 I [auth C] SDF format, chain E [auth C] MOL2 format, chain I [auth C] MOL2 format, chain E [auth C] mmCIF format, chain I [auth C] mmCIF format, chain E [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 R [auth A] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain S [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] MOL2 format, chain H [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth D] MOL2 format, chain R [auth A] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain S [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] mmCIF format, chain H [auth C] mmCIF format, chain L [auth D] mmCIF format, chain N [auth D] mmCIF format, chain R [auth A] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain S [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A]	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 J [auth D] SDF format, chain K [auth D] SDF format, chain T [auth A] SDF format, chain W [auth B] SDF format, chain G [auth C] SDF format, chain F [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] MOL2 format, chain G [auth C] MOL2 format, chain F [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] mmCIF format, chain G [auth C] mmCIF format, chain F [auth C]	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]