MolNFT v1 · #86285 · protein

Structure of the PHACTR1 rpel domain bound to G-actin

4B1Z · Actin, alpha skeletal muscle: “Structure of the PHACTR1 rpel domain bound to G-actin”. X-ray diffraction, 2 ligands (ATP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #86285 on GenesisL1: 3D structure, binding sites and…

PDB: 4B1Z
Type: protein
Length: 2,351 residues
Chains: 8
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: ATP, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 7 distinct chains · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Actin, alpha skeletal muscle	protein	335	47% helix, 19% strand	P68135
B, F	Actin, alpha skeletal muscle	protein	357	45% helix, 20% strand	P68135
C	Actin, alpha skeletal muscle	protein	370	44% helix, 20% strand	P68135
D	Actin, alpha skeletal muscle	protein	356	46% helix, 20% strand	P68135
E	Actin, alpha skeletal muscle	protein	359	45% helix, 21% strand	P68135
M	Phosphatase and actin regulator 1	protein	110	61% helix, 0% strand	G5E8P7
N	Phosphatase and actin regulator 1	protein	107	60% helix, 0% strand	G5E8P7

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, M, C, D, E, N, F
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 8 copies · chains A, B, C, E, N, F, M

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	968	0.85	0.87	116	ATP, MG
2	1045	0.84	0.85	108	ATP, MG
3	1069	0.83	0.84	106	ATP, MG
4	1155	0.81	0.82	109	ATP, MG
5	1044	0.81	0.82	95	GOL

Interfaces

16 interfaces between chains.

F–N · 1670 Å² buried · 23 hydrogen bonds · protein-protein
C–M · 1604 Å² buried · 18 hydrogen bonds · protein-protein
B–M · 1470 Å² buried · 16 hydrogen bonds · protein-protein
E–N · 1357 Å² buried · 17 hydrogen bonds · protein-protein
A–M · 797 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4B1Z · Structure of the Phactr1 RPEL domain bound to G-actin · the same entry in another collection · chain N against N, 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 G5E8P7
Elsewhere: RCSB PDB 4B1Z · PDBe 4B1Z · UniProt P68135 · UniProt G5E8P7

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