MolNFT v1 · #97466 · protein

Crystal structure of ssopox W263M

4KEU · Aryldialkylphosphatase: “Crystal structure of ssopox W263M”. X-ray diffraction, 2 ligands (FE2, CO), 9 pockets (best druggability 0.84). MolNFT v1 #97466 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4KEU
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: 9 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Aryldialkylphosphatase (EC 3.1.8.1)	protein	314	47% 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 · 6 copies · chains A, C, B, D
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D

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

Pockets

9 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	823	0.84	0.86	77	CO, EDO
2	414	0.83	0.90	39	EDO
3	567	0.75	0.82	67	empty
4	373	0.71	0.83	52	empty
5	346	0.70	0.83	50	EDO

Interfaces

3 interfaces between chains.

B–D · 1853 Å² buried · 35 hydrogen bonds · protein-protein
A–C · 1832 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 471 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (carboxylation).

Compared structures

4KEU · Crystal structure of SsoPox W263M · 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 4KEU · PDBe 4KEU · UniProt Q97VT7

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