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Crystal structure of wild-type mal rpel domain in complex with five G- actins

Analyse Crystal structure of wild-type mal rpel domain in complex with five G- actins in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TPQ
Type: protein
Length: 1,855 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle; Mal
UniProt: P68135
Ligands: ATP, CA
Pockets: 13 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 46% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Actin, alpha skeletal muscle	protein	346	45% helix, 18% strand	P68135
B, C	Actin, alpha skeletal muscle	protein	358	43% helix, 21% strand	P68135
D	Actin, alpha skeletal muscle	protein	358	44% helix, 21% strand	P68135
E	Actin, alpha skeletal muscle	protein	318	47% helix, 17% strand	P68135
M	Mal	protein	117	61% helix, 0% strand	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains A, M, B, C, D, E
CA · Calcium ion · metal · 5 copies · chains A, B, C, D, E

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

Pockets

13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1040	0.85	0.86	99	ATP, CA
2	1120	0.82	0.83	130	ATP, CA
3	414	0.75	0.85	53	ATP, CA
4	649	0.74	0.81	61	empty
5	335	0.73	0.85	39	empty

Interfaces

11 interfaces between chains.

A–M · 1596 Å² buried · 17 hydrogen bonds · protein-protein
B–M · 1215 Å² buried · 8 hydrogen bonds · protein-protein
D–M · 1074 Å² buried · 13 hydrogen bonds · protein-protein
C–M · 715 Å² buried · 13 hydrogen bonds · protein-protein
E–M · 607 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3TPQ · Crystal structure of wild-type MAL RPEL domain in complex with five G-actins · 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 E 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
Elsewhere: RCSB PDB 3TPQ · PDBe 3TPQ · UniProt P68135

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