8WWV

1-naphthylamine GS in complex with ADP and MetSox-P

PDB DOI: https://doi.org/10.2210/pdb8WWV/pdb

Classification: LIGASE
Organism(s): Pseudomonas lactis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-26 Released: 2024-01-03
Deposition Author(s): Zhang, S.T., Zhou, N.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.232
R-Value Work: 0.212
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of the 1-naphthylamine biodegradation pathway reveals a glutamine synthetase-like protein that catalyzes 1-naphthylamine glutamylation

Zhang, S.T., Zhou, N.Y.

To be published.

Macromolecule Content

Total Structure Weight: 346.53 kDa
Atom Count: 23,878
Modelled Residue Count: 2,937
Deposited Residue Count: 3,060
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine synthetase	A, B, C, D, E A, B, C, D, E, F	510	Pseudomonas lactis	Mutation(s): 0 Gene Names: HBO18_29070
UniProt
Find proteins for A0A7Y1Q2L1 (Pseudomonas lactis) Explore A0A7Y1Q2L1 Go to UniProtKB: A0A7Y1Q2L1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7Y1Q2L1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain FA [auth F] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D]	AA [auth E] FA [auth F] G [auth A] L [auth B] Q [auth C] AA [auth E], FA [auth F], G [auth A], L [auth B], Q [auth C], V [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D]
P3S (Subject of Investigation/LOI) Query on P3S Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain GA [auth F] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain W [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D]	BA [auth E] GA [auth F] H [auth A] M [auth B] R [auth C] BA [auth E], GA [auth F], H [auth A], M [auth B], R [auth C], W [auth D]	L-METHIONINE-S-SULFOXIMINE PHOSPHATE C₅ H₁₃ N₂ O₆ P S QQFOFBSCSWFFPB-NMAPHRJESA-N		Interactions Focus chain BA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain HA [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D]	CA [auth E] DA [auth E] HA [auth F] I [auth A] IA [auth F] CA [auth E], DA [auth E], HA [auth F], I [auth A], IA [auth F], J [auth A], N [auth B], O [auth B], S [auth C], T [auth C], X [auth D], Y [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Focus chain Y [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain JA [auth F] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D]	EA [auth E] JA [auth F] K [auth A] P [auth B] U [auth C] EA [auth E], JA [auth F], K [auth A], P [auth B], U [auth C], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain JA [auth F] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth E] Focus chain JA [auth F] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain Z [auth D]