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Human metavinculin (residues 959-1134) in complex with PIP2

Analyse Human metavinculin (residues 959-1134) in complex with PIP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5L0C
Type: protein
Length: 692 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vinculin
UniProt: P18206
Ligands: PIO, PO4
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 71% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vinculin	protein	176	72% helix, 2% strand	P18206
B, C	Vinculin	protein	175	69% helix, 1% strand	P18206
D	Vinculin	protein	166	71% helix, 1% 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 · 5 copies · chains A, B, D, C
PO4 · Phosphate ion · ion · 3 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	903	0.82	0.84	96	empty
2	289	0.66	0.82	28	PO4
3	207	0.57	0.80	31	empty
4	178	0.56	0.80	23	empty

Interfaces

6 interfaces between chains.

A–B · 761 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 575 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 463 Å² buried · 1 hydrogen bond · protein-protein
A–C · 187 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 142 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5L0C · Human metavinculin (residues 959-1134) in complex with PIP2 · the same entry in another collection · chain A against A, TM-score 1.00
P18206 · AlphaFold monomer V2.0 prediction for vinculin (P18206) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 5L0C · PDBe 5L0C · UniProt P18206

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