6NVF

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 8

PDB DOI: https://doi.org/10.2210/pdb6NVF/pdb

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

Deposited: 2019-02-05 Released: 2020-02-12
Deposition Author(s): Thompson, A.P., Polyak, S.W., Wegener, K.L., Bruning, J.B.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.230
R-Value Work: 0.185
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Currently 6NVF does not have a validation slider image.

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

Literature

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 8

Thompson, A.P., Polyak, S.W., Wegener, K.L., Bruning, J.B.

To be published.

Macromolecule Content

Total Structure Weight: 95.18 kDa
Atom Count: 7,325
Modelled Residue Count: 909
Deposited Residue Count: 932
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-dependent dethiobiotin synthetase BioD	A, B, C, D	233	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: bioD, Rv1570, MTCY336.33c EC: 6.3.3.3
UniProt
Find proteins for P9WPQ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPQ5 Go to UniProtKB: P9WPQ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPQ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L5J (Subject of Investigation/LOI) Query on L5J Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain M [auth D] MOL2 format, chain G [auth B] MOL2 format, chain M [auth D]	G [auth B], M [auth D]	(4-{[(1R,2R)-2-(carboxymethyl)cyclopentyl]methyl}phenyl)acetic acid C₁₆ H₂₀ O₄ QKXFMUHRVZWRPO-ZIAGYGMSSA-N		Interactions Focus chain G [auth B] Focus chain M [auth D] Interactions & Density Focus chain G [auth B] Focus chain M [auth D]
L5A (Subject of Investigation/LOI) Query on L5A Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D]	E [auth A], H [auth B], J [auth C], L [auth D]	(4-{[(1S,2S)-2-(carboxymethyl)cyclopentyl]methyl}phenyl)acetic acid C₁₆ H₂₀ O₄ QKXFMUHRVZWRPO-KBPBESRZSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D]	F [auth A], I [auth B], K [auth C], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain N [auth D]