MolNFT v1 · #125146 · protein

Human METAVINCULIN(RESIDUES 959-1130) in complex with PIP2

5L0D: “Human METAVINCULIN(RESIDUES 959-1130) in complex with PIP2”. X-ray diffraction, 1 ligand (PIO), 6 pockets (best druggability 0.75). MolNFT v1 #125146 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L0D
Type: protein
Length: 672 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vinculin
UniProt: P18206
Ligands: PIO
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 76% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vinculin	protein	168	77% helix, 1% strand	P18206
B	Vinculin	protein	170	74% helix, 1% strand	P18206
C	Vinculin	protein	168	76% helix, 1% strand	P18206
D	Vinculin	protein	166	78% 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, D

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

Pockets

6 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	945	0.75	0.78	77	PIO
2	503	0.69	0.79	43	empty
3	466	0.68	0.79	55	empty
4	124	0.46	0.78	23	empty
5	96	0.41	0.78	25	empty

Interfaces

5 interfaces between chains.

A–C · 905 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 497 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 426 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 199 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 38 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5L0D · Human Metavinculin(residues 959-1130) in complex with PIP2 · the same entry in another collection · chain D against D, TM-score 1.00
P18206 · AlphaFold monomer V2.0 prediction for vinculin (P18206) · a predicted model of the same protein · chain C 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 5L0D · PDBe 5L0D · UniProt P18206

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