Research workbench

Succinate complex of atsk

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

PDB: 1VZ5
Type: protein
Length: 996 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative alkylsulfatase atsk
UniProt: Q9WWU5
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Putative alkylsulfatase atsk	protein	254	22% helix, 30% strand	Q9WWU5
C	Putative alkylsulfatase atsk	protein	244	22% helix, 31% strand	Q9WWU5
D	Putative alkylsulfatase atsk	protein	244	22% helix, 31% strand	Q9WWU5

Ligands and binding sites

SIN · Succinic acid · additive · 4 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	784	0.71	0.77	63	empty
2	833	0.71	0.76	61	empty
3	290	0.63	0.80	29	empty
4	296	0.63	0.80	32	empty
5	206	0.59	0.80	36	SIN

Interfaces

5 interfaces between chains.

B–C · 882 Å² buried · 21 hydrogen bonds · protein-protein
A–D · 879 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 703 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 692 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 38 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1VZ5 · Succinate Complex of AtsK · the same entry in another collection · chain D against D, TM-score 1.00
Q9WWU5 · AlphaFold monomer V2.0 prediction for alpha-ketoglutarate-dependent sulfate ester… · a predicted model of the same protein · chain C 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 Q9WWU5
Elsewhere: RCSB PDB 1VZ5 · PDBe 1VZ5 · UniProt Q9WWU5

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