Research workbench

Crystal structure of actin capping protein in complex with V-1

Analyse Crystal structure of actin capping protein in complex with V-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AAA
Type: protein
Length: 634 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: F-actin-capping protein subunit alpha-1; F-actin-capping protein subunit beta isoforms 1…
UniProt: P13127, P14315, P58546
Pockets: 9 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	F-actin-capping protein subunit alpha-1	protein	267	40% helix, 35% strand	P13127
B	F-actin-capping protein subunit beta isoforms 1 and 2	protein	250	39% helix, 34% strand	P14315
C	Myotrophin	protein	117	52% helix, 0% strand	P58546

Ligands and binding sites

IPA · Isopropyl alcohol · additive · 2 copies · chains B

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

Pockets

9 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	252	0.62	0.81	35	empty
2	249	0.57	0.78	27	empty
3	91	0.54	0.85	24	empty
4	228	0.53	0.77	40	empty
5	149	0.45	0.76	20	empty

Interfaces

3 interfaces between chains.

A–B · 3718 Å² buried · 56 hydrogen bonds · protein-protein
B–C · 514 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 491 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3AAA · Crystal Structure of Actin capping protein in complex with V-1 · the same entry in another collection · chain A against A, TM-score 1.00
P58546 · AlphaFold monomer V2.0 prediction for myotrophin (P58546) · a predicted model of the same protein · chain C against A, TM-score 0.97
P13127 · AlphaFold monomer V2.0 prediction for F-actin-capping protein subunit alpha-1 (P13127) · a predicted model of the same protein · chain A against A, TM-score 0.94
P14315 · AlphaFold monomer V2.0 prediction for F-actin-capping protein subunit beta isoforms 1 and… · a predicted model of the same protein · chain B against A, TM-score 0.92

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 P13127
Every structure of UniProt P14315
Every structure of UniProt P58546
Elsewhere: RCSB PDB 3AAA · PDBe 3AAA · UniProt P13127 · UniProt P14315 · UniProt P58546

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