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Crystal structure of archaeal actin

Analyse Crystal structure of archaeal actin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4BQL
Type: protein
Length: 1,720 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ACTIN/ACTIN family protein
UniProt: A3MWN5
Ligands: ADP, MG
Pockets: 17 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ACTIN/ACTIN family protein	protein	436	43% helix, 19% strand	A3MWN5
B	ACTIN/ACTIN family protein	protein	430	43% helix, 20% strand	A3MWN5
C, D	ACTIN/ACTIN family protein	protein	427	44% helix, 19% strand	A3MWN5

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, D
MG · Magnesium ion · metal · chains B

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

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1060	0.81	0.83	116	empty
2	642	0.74	0.80	75	ADP
3	628	0.71	0.79	64	ADP
4	609	0.71	0.79	67	MG, ADP
5	278	0.63	0.81	39	empty

Interfaces

4 interfaces between chains.

B–C · 1319 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1161 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 257 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 211 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

4BQL · Crystal structure of archaeal actin · the same entry in another collection · chain D against D, TM-score 1.00
A3MWN5 · AlphaFold monomer V2.0 prediction for crenactin (A3MWN5) · a predicted model of the same protein · chain D against A, TM-score 0.97

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 A3MWN5
Elsewhere: RCSB PDB 4BQL · PDBe 4BQL · UniProt A3MWN5

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