7NNV

Crystal structure of Mycobacterium tuberculosis ArgF in complex with carbamoyl phosphate.

PDB DOI: https://doi.org/10.2210/pdb7NNV/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-02-25 Released: 2021-06-30
Deposition Author(s): Mendes, V., Gupta, P., Burgess, A., Sebastian-Perez, V., Cattermole, E., Meghir, C., Blundell, T.L.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.180
R-Value Work: 0.161
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis

Gupta, P., Thomas, S.E., Zaidan, S.A., Pasillas, M.A., Cory-Wright, J., Sebastian-Perez, V., Burgess, A., Cattermole, E., Meghir, C., Abell, C., Coyne, A.G., Jacobs, W.R., Blundell, T.L., Tiwari, S., Mendes, V.

(2021) Comput Struct Biotechnol J 19: 3491-3506

DOI: https://doi.org/10.1016/j.csbj.2021.06.006

Macromolecule Content

Total Structure Weight: 201.32 kDa
Atom Count: 15,612
Modelled Residue Count: 1,814
Deposited Residue Count: 1,854
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ornithine carbamoyltransferase	A, B, C, D, E A, B, C, D, E, F	309	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: argF, Rv1656, MTCY06H11.21 EC: 2.1.3.3
UniProt
Find proteins for P9WIT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIT9 Go to UniProtKB: P9WIT9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WIT9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CP (Subject of Investigation/LOI) Query on CP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain V [auth E] SDF format, chain Z [auth F] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Z [auth F]	H [auth A] M [auth B] O [auth C] R [auth D] V [auth E] H [auth A], M [auth B], O [auth C], R [auth D], V [auth E], Z [auth F]	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER C H₄ N O₅ P FFQKYPRQEYGKAF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain Z [auth F] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain V [auth E] Focus chain Z [auth F]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain W [auth E] SDF format, chain Y [auth E] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth E]	G [auth A] I [auth A] L [auth B] N [auth C] Q [auth D] G [auth A], I [auth A], L [auth B], N [auth C], Q [auth D], S [auth D], U [auth E], W [auth E], Y [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth E] Focus chain Y [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth E] Focus chain Y [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth E]	AA [auth F] J [auth A] K [auth A] P [auth C] T [auth D] AA [auth F], J [auth A], K [auth A], P [auth C], T [auth D], X [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E]