Research workbench

Structure of the PHACTR1 rpel-3 bound to G-actin

Analyse Structure of the PHACTR1 rpel-3 bound to G-actin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4B1Y
Type: protein
Length: 394 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle; Phosphatase and actin regulator 1
UniProt: P68135, G5E8P7
Ligands: LAB, ATP, MG
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Actin, alpha skeletal muscle	protein	364	46% helix, 20% strand	P68135
M	Phosphatase and actin regulator 1	protein	30	57% helix, 0% strand	G5E8P7

Ligands and binding sites

LAB · Latrunculin B · ligand · chains B
ATP · Adenosine-5'-triphosphate · ligand · chains B
MG · Magnesium ion · metal · chains B
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, M
1PE · Pentaethylene glycol · additive · chains B, M
GOL · Glycerol · additive · chains B
P6G · Hexaethylene glycol · additive · chains B, M

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

Pockets

4 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	385	0.72	0.83	56	LAB, ATP, MG
2	117	0.59	0.85	25	1PE
3	218	0.54	0.77	21	PEG, P6G
4	79	0.37	0.77	21	empty

Interfaces

1 interface between chains.

B–M · 969 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4B1Y · Structure of the Phactr1 RPEL-3 bound to G-actin · 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 0.98

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 G5E8P7
Elsewhere: RCSB PDB 4B1Y · PDBe 4B1Y · UniProt P68135 · UniProt G5E8P7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.