MolNFT v1 · #167228 · protein

Cryo-EM structure of F-ACTIN/PLASTIN2-ABD2 complex

6VEC · Actin, alpha skeletal muscle: “Cryo-EM structure of F-ACTIN/PLASTIN2-ABD2 complex”. Electron microscopy, 2 ligands (ADP, MG), 20 pockets (best druggability 0.80). MolNFT v1 #167228 on GenesisL1: 3D structure, binding sites and…

PDB: 6VEC
Type: protein
Length: 6,721 residues
Chains: 22
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle; LCP1
UniProt: P68135, V9HWJ7
Ligands: ADP, MG
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 2 distinct chains · 48% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K	Actin, alpha skeletal muscle	protein	370	43% helix, 20% strand	P68135
a, b, c, d, e, f, g, h, i, j, k	LCP1	protein	241	56% helix, 0% strand	V9HWJ7

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 11 copies · chains A, B, C, D, E, F, G, H, I, J, K
MG · Magnesium ion · metal · 11 copies · chains A, B, C, D, E, F, G, H, I, J, K

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	380	0.80	0.89	55	ADP, MG
2	814	0.80	0.83	87	empty
3	386	0.79	0.88	55	ADP, MG
4	364	0.79	0.89	53	ADP, MG
5	407	0.79	0.88	59	ADP, MG

Interfaces

39 interfaces between chains.

E–I · 1225 Å² buried · 13 hydrogen bonds · protein-protein
F–J · 1218 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 1215 Å² buried · 9 hydrogen bonds · protein-protein
C–G · 1212 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 1206 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6VEC · Cryo-EM structure of F-actin/Plastin2-ABD2 complex · the same entry in another collection · chain K against K, TM-score 1.00

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 P68135
Every structure of UniProt V9HWJ7
Elsewhere: RCSB PDB 6VEC · PDBe 6VEC · UniProt P68135 · UniProt V9HWJ7

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