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Crystal structure of the gntr-hutc family member yvoa from bacillus subtilis

Analyse Crystal structure of the gntr-hutc family member yvoa from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WV0
Type: protein
Length: 2,378 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hth-type transcriptional repressor yvoa
UniProt: O34817
Ligands: SO4
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 7 distinct chains · 31% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hth-type transcriptional repressor yvoa	protein	243	32% helix, 33% strand	O34817
B, C, D, I	Hth-type transcriptional repressor yvoa	protein	242	32% helix, 32% strand	O34817
E	Hth-type transcriptional repressor yvoa	protein	234	33% helix, 32% strand	O34817
F	Hth-type transcriptional repressor yvoa	protein	237	33% helix, 33% strand	O34817
G	Hth-type transcriptional repressor yvoa	protein	237	32% helix, 30% strand	O34817
H	Hth-type transcriptional repressor yvoa	protein	224	26% helix, 32% strand	O34817
J	Hth-type transcriptional repressor yvoa	protein	235	29% helix, 28% strand	O34817

Ligands and binding sites

SO4 · Sulfate ion · ion · 15 copies · chains A, I, B, D, C, F, E, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	631	0.77	0.83	72	empty
2	272	0.77	0.89	59	empty
3	122	0.74	0.94	35	SO4
4	847	0.74	0.78	123	empty
5	493	0.72	0.82	89	SO4

Interfaces

9 interfaces between chains.

E–F · 1851 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 1828 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 1813 Å² buried · 35 hydrogen bonds · protein-protein
B–D · 1592 Å² buried · 15 hydrogen bonds · protein-protein
H–I · 1522 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

2WV0 · Crystal structure of the GntR-HutC family member YvoA from Bacillus subtilis · the same entry in another collection · chain J against J, TM-score 1.00
O34817 · AlphaFold monomer V2.0 prediction for hth-type transcriptional repressor nagr (O34817) · a predicted model of the same protein · chain E against A, TM-score 0.67

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 O34817
Elsewhere: RCSB PDB 2WV0 · PDBe 2WV0 · UniProt O34817

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