MolNFT v1 · #166440 · protein

Metavinculin abd-F-actin complex

6UPW: “Metavinculin abd-F-actin complex”. Electron microscopy, 2 ligands (ADP, MG), 20 pockets (best druggability 0.79). MolNFT v1 #166440 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6UPW
Type: protein
Length: 2,152 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vinculin; Actin, alpha skeletal muscle
UniProt: P18206, P68139
Ligands: ADP, MG
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 2 distinct chains · 50% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	Vinculin	protein	151	74% helix, 0% strand	P18206
C, B, A, D, E	Actin, alpha skeletal muscle	protein	370	40% helix, 20% strand	P68139

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains C, B, A, D, E
MG · Magnesium ion · metal · 5 copies · chains C, B, A, D, E

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	717	0.79	0.83	75	empty
2	630	0.77	0.83	78	empty
3	313	0.77	0.88	55	ADP, MG
4	316	0.76	0.88	49	ADP, MG
5	294	0.76	0.88	48	ADP, MG

Interfaces

11 interfaces between chains.

L–A · 1365 Å² buried · 10 hydrogen bonds · protein-protein
C–M · 1320 Å² buried · 7 hydrogen bonds · protein-protein
C–A · 1222 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 1221 Å² buried · 10 hydrogen bonds · protein-protein
C–E · 1218 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified, 1 covalent (methylation, covalent ligand).

Compared structures

6UPW · Metavinculin ABD-F-actin complex · the same entry in another collection · chain E against E, TM-score 1.00
P68139 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68139) · a predicted model of the same protein · chain D 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
Every structure of UniProt P68139
Elsewhere: RCSB PDB 6UPW · PDBe 6UPW · UniProt P18206 · UniProt P68139

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