MolNFT v1 · #69279 · protein

Vibrio cholerae vpst bound to C-di-gmp

3KLO · Transcriptional regulator vpst: “Vibrio cholerae vpst bound to C-di-gmp”. X-ray diffraction, 1 ligand (C2E), 15 pockets (best druggability 0.57). MolNFT v1 #69279 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3KLO
Type: protein
Length: 819 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional regulator vpst
UniProt: Q9KKZ8
Ligands: C2E
Pockets: 15 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcriptional regulator vpst	protein	217	52% helix, 14% strand	Q9KKZ8
B	Transcriptional regulator vpst	protein	216	55% helix, 14% strand	Q9KKZ8
C	Transcriptional regulator vpst	protein	213	53% helix, 15% strand	Q9KKZ8
D	Transcriptional regulator vpst	protein	173	46% helix, 18% strand	Q9KKZ8

Ligands and binding sites

C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 4 copies · chains A, B, C, D
TAR · D(-)-tartaric acid · additive · 2 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	217	0.57	0.79	29	empty
2	243	0.56	0.78	34	empty
3	98	0.51	0.82	16	empty
4	137	0.48	0.78	17	empty
5	73	0.47	0.83	18	empty

Interfaces

4 interfaces between chains.

A–B · 800 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 792 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 580 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 19 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3KLO · Vibrio cholerae VpsT bound to c-di-GMP · 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 Q9KKZ8
Elsewhere: RCSB PDB 3KLO · PDBe 3KLO · UniProt Q9KKZ8

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