Research workbench

LOKIPROFILIN2/RABBIT actin complex

Analyse LOKIPROFILIN2/RABBIT actin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZZB
Type: protein
Length: 997 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle; Uncharacterized protein
UniProt: P68135, A0A0F8XMN8
Ligands: LAB, ATP, CA
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Actin, alpha skeletal muscle	protein	364	43% helix, 20% strand	P68135
A	Uncharacterized protein	protein	134	28% helix, 31% strand	A0A0F8XMN8
D	Actin, alpha skeletal muscle	protein	363	45% helix, 20% strand	P68135
C	Uncharacterized protein	protein	136	26% helix, 30% strand	A0A0F8XMN8

Ligands and binding sites

LAB · Latrunculin B · ligand · 2 copies · chains B, D
ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, D
CA · Calcium ion · metal · 2 copies · chains B, D

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	416	0.74	0.84	54	LAB, ATP, CA
2	403	0.74	0.85	48	LAB, ATP, CA
3	768	0.72	0.78	90	empty
4	543	0.69	0.79	54	empty
5	348	0.57	0.76	50	empty

Interfaces

3 interfaces between chains.

B–A · 693 Å² buried · 4 hydrogen bonds · protein-protein
D–C · 624 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 312 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5ZZB · LokiProfilin2/Rabbit Actin Complex · the same entry in another collection · chain B against B, TM-score 1.00
P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 A0A0F8XMN8
Elsewhere: RCSB PDB 5ZZB · PDBe 5ZZB · UniProt P68135 · UniProt A0A0F8XMN8

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