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Crystal structure of cvir (chromobacterium violaceum 12472) ligand- binding domain bound to C10-hsl

Analyse Crystal structure of cvir (chromobacterium violaceum 12472) ligand- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QP8
Type: protein
Length: 728 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cvir transcriptional regulator
UniProt: Q7NQP7
Ligands: HL0
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cvir transcriptional regulator	protein	179	45% helix, 20% strand	Q7NQP7
B, D	Cvir transcriptional regulator	protein	184	45% helix, 18% strand	Q7NQP7
C	Cvir transcriptional regulator	protein	181	45% helix, 19% strand	Q7NQP7

Ligands and binding sites

HL0 · N-[(3S)-2-oxotetrahydrofuran-3-yl]decanamide · ligand · 4 copies · chains A, D, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	597	0.78	0.84	68	HL0
2	309	0.69	0.83	45	empty
3	124	0.67	0.88	24	HL0
4	111	0.67	0.89	23	HL0
5	112	0.67	0.89	23	HL0

Interfaces

5 interfaces between chains.

C–D · 1504 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1340 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 651 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 303 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 114 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3QP8 · Crystal structure of CviR (Chromobacterium violaceum 12472) ligand-binding domain bound… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q7NQP7
Elsewhere: RCSB PDB 3QP8 · PDBe 3QP8 · UniProt Q7NQP7

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