8J4X

Structure of Mycobacterium tuberculosis NrdF2:NrdIcomplex (oxidised) determined at 3 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb8J4X/pdb

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

Deposited: 2023-04-21 Released: 2024-10-09
Deposition Author(s): Yadav, L.R., Mande, S.C.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.04 Å
R-Value Free: 0.254
R-Value Work: 0.219
R-Value Observed: 0.221

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural insights into the initiation of free radical formation in the Class Ib ribonucleotide reductases in Mycobacteria

Yadav, L.R., Sharma, V., Shanmugam, M., Mande, S.C.

(2024) Curr Res Struct Biol 8: 100157

DOI: https://doi.org/10.1016/j.crstbi.2024.100157

Macromolecule Content

Total Structure Weight: 256.84 kDa
Atom Count: 16,024
Modelled Residue Count: 1,971
Deposited Residue Count: 2,244
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase subunit beta nrdF2	A, B, C, D, E A, B, C, D, E, F	324	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: nrdF2 EC: 1.17.4.1
UniProt
Find proteins for P9WH71 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WH71 Go to UniProtKB: P9WH71
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WH71
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein NrdI	G, H [auth I]	150	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: nrdI
UniProt
Find proteins for P9WIZ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIZ3 Go to UniProtKB: P9WIZ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WIZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain DA [auth I] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth I]	CA [auth G], DA [auth I]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain CA [auth G] Focus chain DA [auth I] Interactions & Density Focus chain CA [auth G] Focus chain DA [auth I]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain Y [auth F] MOL2 format, chain Q [auth C] MOL2 format, chain Y [auth F]	Q [auth C], Y [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Focus chain Y [auth F] Interactions & Density Focus chain Q [auth C] Focus chain Y [auth F]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F]	AA [auth F] I [auth A] J [auth A] L [auth B] M [auth B] AA [auth F], I [auth A], J [auth A], L [auth B], M [auth B], O [auth C], P [auth C], S [auth D], T [auth D], V [auth E], W [auth E], Z [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain Z [auth F]
OH (Subject of Investigation/LOI) Query on OH Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E]	BA [auth F] K [auth A] N [auth B] R [auth C] U [auth D] BA [auth F], K [auth A], N [auth B], R [auth C], U [auth D], X [auth E]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M		Interactions Focus chain BA [auth F] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain BA [auth F] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]