MolNFT v1 · #76574 · protein

Crystal structure of cvir bound to antagonist chlorolactone (cl)

3QP5 · Cvir transcriptional regulator: “Crystal structure of cvir bound to antagonist chlorolactone (cl)”. X-ray diffraction, 1 ligand (HLC), 15 pockets (best druggability 0.83). MolNFT v1 #76574 on GenesisL1: 3D structure, binding sites…

PDB: 3QP5
Type: protein
Length: 966 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cvir transcriptional regulator
UniProt: D3W065
Ligands: HLC
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cvir transcriptional regulator	protein	251	44% helix, 14% strand	D3W065
B	Cvir transcriptional regulator	protein	238	48% helix, 11% strand	D3W065
C	Cvir transcriptional regulator	protein	239	51% helix, 14% strand	D3W065
D	Cvir transcriptional regulator	protein	238	48% helix, 13% strand	D3W065

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1097	0.83	0.84	116	HLC
2	634	0.74	0.81	62	empty
3	323	0.74	0.85	42	HLC
4	327	0.71	0.83	39	HLC
5	327	0.70	0.83	36	HLC

Interfaces

5 interfaces between chains.

A–B · 2263 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 2176 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 456 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 431 Å² buried · 11 hydrogen bonds · protein-protein
A–D · 284 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3QP5 · Crystal structure of CviR bound to antagonist chlorolactone (CL) · the same entry in another collection · chain A against A, TM-score 1.00

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 D3W065
Elsewhere: RCSB PDB 3QP5 · PDBe 3QP5 · UniProt D3W065

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