6NN0

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with 2'-deoxycytidine and fragment degradation product B9D

PDB DOI: https://doi.org/10.2210/pdb6NN0/pdb

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

Deposited: 2019-01-14 Released: 2020-01-22
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: 2.34 Å
R-Value Free: 0.296
R-Value Work: 0.222
R-Value Observed: 0.225

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with 2'-deoxycytidine and B9D

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

To be published.

Macromolecule Content

Total Structure Weight: 96.29 kDa
Atom Count: 6,692
Modelled Residue Count: 907
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KSP Query on KSP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain U [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D]	G [auth A], L [auth B], P [auth C], U [auth D]	[(1R,2S)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid C₁₄ H₁₆ O₄ LULBZYDRYZGRST-ZJUUUORDSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth D]
KSJ Query on KSJ Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain T [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain T [auth D]	F [auth A], K [auth B], O [auth C], T [auth D]	[(1S,2R)-2-(2-hydroxybenzene-1-carbonyl)cyclopentyl]acetic acid C₁₄ H₁₆ O₄ LULBZYDRYZGRST-VHSXEESVSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D]
CTN Query on CTN Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain S [auth D] MOL2 format, chain J [auth B] MOL2 format, chain S [auth D] mmCIF format, chain J [auth B] mmCIF format, chain S [auth D]	J [auth B], S [auth D]	4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE C₉ H₁₃ N₃ O₅ UHDGCWIWMRVCDJ-XVFCMESISA-N		Interactions Focus chain J [auth B] Focus chain S [auth D] Interactions & Density Focus chain J [auth B] Focus chain S [auth D]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	E [auth A] H [auth B] I [auth B] M [auth C] N [auth C] E [auth A], H [auth B], I [auth B], M [auth C], N [auth C], Q [auth D], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth D]