MolNFT v1 · #111156 · protein

Crystal structure of RV0880

4YIF · Marr family protein RV0880: “Crystal structure of RV0880”. X-ray diffraction, 8 pockets (best druggability 0.87). MolNFT v1 #111156 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YIF
Type: protein
Length: 813 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Marr family protein RV0880
UniProt: P9WMF1
Pockets: 8 · best druggability 0.87

Structure

x-ray diffraction · 6 distinct chains · 68% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Marr family protein RV0880	protein	140	66% helix, 3% strand	P9WMF1
B	Marr family protein RV0880	protein	141	68% helix, 8% strand	P9WMF1
C	Marr family protein RV0880	protein	139	66% helix, 8% strand	P9WMF1
D	Marr family protein RV0880	protein	132	67% helix, 5% strand	P9WMF1
E	Marr family protein RV0880	protein	131	69% helix, 5% strand	P9WMF1
F	Marr family protein RV0880	protein	130	70% helix, 7% strand	P9WMF1

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.87	0.89	107	empty
2	797	0.85	0.88	90	empty
3	281	0.77	0.89	52	empty
4	72	0.57	0.88	24	empty
5	69	0.53	0.86	18	empty

Interfaces

11 interfaces between chains.

E–F · 2870 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2849 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 2690 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 473 Å² buried · 14 hydrogen bonds · protein-protein
A–F · 467 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4YIF · Crystal structure of Rv0880 · the same entry in another collection · chain F against F, TM-score 1.00
P9WMF1 · AlphaFold monomer V2.0 prediction for uncharacterized hth-type transcriptional regulator… · a predicted model of the same protein · chain F against A, TM-score 0.96

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 P9WMF1
Elsewhere: RCSB PDB 4YIF · PDBe 4YIF · UniProt P9WMF1

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