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Crystal structure of ssopox W263F

Analyse Crystal structure of ssopox W263F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KEZ
Type: protein
Length: 1,256 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aryldialkylphosphatase
EC: 3.1.8.1
UniProt: Q97VT7
Ligands: FE2, CO
Pockets: 7 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Aryldialkylphosphatase (EC 3.1.8.1)	protein	314	49% helix, 14% strand	Q97VT7

Ligands and binding sites

FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 11 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · chains C

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

Pockets

7 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	1133	0.85	0.85	123	GOL, EDO
2	880	0.83	0.85	81	GOL
3	405	0.68	0.80	48	GOL
4	173	0.41	0.73	24	empty
5	154	0.39	0.72	21	empty

Interfaces

3 interfaces between chains.

A–D · 1864 Å² buried · 40 hydrogen bonds · protein-protein
B–C · 1860 Å² buried · 36 hydrogen bonds · protein-protein
A–C · 178 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (carboxylation).

Compared structures

4KEZ · Crystal structure of SsoPox W263F · the same entry in another collection · chain A against A, TM-score 1.00
Q97VT7 · AlphaFold monomer V2.0 prediction for aryldialkylphosphatase (Q97VT7) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q97VT7
Elsewhere: RCSB PDB 4KEZ · PDBe 4KEZ · UniProt Q97VT7

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