MolNFT v1 · #125149 · protein

Human metavinculin mvt Q971R, R975D, T978R mutant (residues 959-1134) in complex with PIP2

5L0G: “Human metavinculin mvt Q971R, R975D, T978R mutant (residues 959-1134) in complex with PIP2”. X-ray diffraction, 1 ligand (PIO), 5 pockets (best druggability 0.77). MolNFT v1 #125149 on GenesisL1: 3D structure, binding sites and…

PDB: 5L0G
Type: protein
Length: 685 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vinculin
UniProt: P18206
Ligands: PIO
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 74% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vinculin	protein	172	73% helix, 2% strand	P18206
B	Vinculin	protein	172	74% helix, 2% strand	P18206
C	Vinculin	protein	171	76% helix, 2% strand	P18206
D	Vinculin	protein	170	75% helix, 2% 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 · 2 copies · chains A, B, C, D

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

Pockets

5 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	699	0.77	0.82	73	empty
2	162	0.60	0.83	27	empty
3	112	0.47	0.79	19	empty
4	54	0.31	0.76	12	empty
5	65	0.28	0.73	17	empty

Interfaces

5 interfaces between chains.

A–C · 653 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 377 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 341 Å² buried · 1 hydrogen bond · protein-protein
A–D · 142 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 86 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5L0G · Human metavinculin MVt Q971R, R975D, T978R mutant (residues 959-1134) 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 0.98

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 5L0G · PDBe 5L0G · UniProt P18206

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