MolNFT v1 · #140553 · protein

Crystal structure of LOKIPROFILIN1/RABBIT actin complex

5YEE · Actin, alpha skeletal muscle: “Crystal structure of LOKIPROFILIN1/RABBIT actin complex”. X-ray diffraction, 3 ligands (LAB, ATP, MG), 3 pockets (best druggability 0.74). MolNFT v1 #140553 on GenesisL1: 3D structure, binding sites…

PDB: 5YEE
Type: protein
Length: 495 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle; Uncharacterized protein
UniProt: P68135, A0A0F8V8L2
Ligands: LAB, ATP, MG
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Actin, alpha skeletal muscle	protein	360	45% helix, 21% strand	P68135
A	Uncharacterized protein	protein	135	27% helix, 30% strand	A0A0F8V8L2

Ligands and binding sites

LAB · Latrunculin B · ligand · chains B
ATP · Adenosine-5'-triphosphate · ligand · chains B
MG · Magnesium ion · metal · chains B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	392	0.74	0.84	55	LAB, ATP, MG
2	701	0.71	0.78	71	empty
3	57	0.61	0.91	22	empty

Interfaces

1 interface between chains.

B–A · 840 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5YEE · Crystal structure of LokiProfilin1/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 A0A0F8V8L2
Elsewhere: RCSB PDB 5YEE · PDBe 5YEE · UniProt P68135 · UniProt A0A0F8V8L2

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