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Crystal structure of mycobacterium tuberculosis marr family protein RV2887 complex with DNA

Analyse Crystal structure of mycobacterium tuberculosis marr family protein RV2887… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HSO
Type: protein + DNA
Length: 551 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized hth-type transcriptional regulator RV2887; DNA (30-mer), the upstream…
UniProt: P9WME9
Pockets: 6 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 74% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Uncharacterized hth-type transcriptional regulator RV2887	protein	122	75% helix, 2% strand	P9WME9
C	Uncharacterized hth-type transcriptional regulator RV2887	protein	125	74% helix, 3% strand	P9WME9
E	DNA (30-mer), the upstream sequence of RV0560C	dna	30	—	—
F	DNA (30-mer), the upstream sequence of RV0560C	dna	30	—	—

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	596	0.70	0.78	68	empty
2	593	0.70	0.78	64	empty
3	167	0.44	0.75	17	empty
4	168	0.44	0.75	18	empty
5	147	0.39	0.73	16	empty

Interfaces

11 interfaces between chains.

A–B · 2006 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1968 Å² buried · 20 hydrogen bonds · protein-protein
E–F · 1391 Å² buried · 154 hydrogen bonds · nucleic-nucleic
C–E · 161 Å² buried · 2 hydrogen bonds · protein-nucleic
D–F · 121 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

5HSO · Crystal structure of MYCOBACTERIUM TUBERCULOSIS MARR FAMILY PROTEIN Rv2887 complex with… · the same entry in another collection · chain F against F, TM-score 1.00
P9WME9 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor RV2887 (P9WME9) · a predicted model of the same protein · chain C against A, TM-score 0.91

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P9WME9
Elsewhere: RCSB PDB 5HSO · PDBe 5HSO · UniProt P9WME9

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