MolNFT v1 · #103791 · protein

Human vinculin (residues 891-1066) in complex with pip

4PR9: “Human vinculin (residues 891-1066) in complex with pip”. X-ray diffraction, 1 ligand (PIO), 10 pockets (best druggability 0.53). MolNFT v1 #103791 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PR9
Type: protein
Length: 1,033 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vinculin
UniProt: P18206
Ligands: PIO
Pockets: 10 · best druggability 0.53

Structure

x-ray diffraction · 5 distinct chains · 72% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vinculin	protein	175	71% helix, 2% strand	P18206
B, D	Vinculin	protein	176	69% helix, 1% strand	P18206
C	Vinculin	protein	174	71% helix, 2% strand	P18206
E	Vinculin	protein	172	72% helix, 2% strand	P18206
F	Vinculin	protein	160	76% helix, 0% strand	P18206

Ligands and binding sites

PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 3 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 3 copies · chains B, C, D

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

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	330	0.53	0.74	36	empty
2	170	0.52	0.79	24	empty
3	183	0.43	0.73	24	empty
4	139	0.41	0.75	17	empty
5	119	0.40	0.75	17	empty

Interfaces

6 interfaces between chains.

A–B · 557 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 475 Å² buried · 5 hydrogen bonds · protein-protein
E–F · 341 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 287 Å² buried · 2 hydrogen bonds · protein-protein
D–E · 66 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4PR9 · Human Vinculin (residues 891-1066) in complex with PIP · the same entry in another collection · chain F against F, TM-score 1.00
P18206 · AlphaFold monomer V2.0 prediction for vinculin (P18206) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P18206
Elsewhere: RCSB PDB 4PR9 · PDBe 4PR9 · UniProt P18206

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