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Crystal structure of ssopox W263I in complex with C10HTL

Analyse Crystal structure of ssopox W263I in complex with C10HTL in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KF1
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: HT5, CO, FE2
Pockets: 12 · best druggability 0.75

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

HT5 · (4S)-4-(decanoylamino)-5-hydroxy-3,4-dihydro-2H-thiophenium · ligand · 4 copies · chains A, B, C, D
CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 18 copies · chains A, C, B, D
EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, C, D

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

Pockets

12 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	977	0.75	0.78	103	HT5, PG4, EDO, GOL
2	669	0.71	0.78	74	EDO, GOL
3	431	0.65	0.78	49	GOL
4	352	0.63	0.79	45	HT5, PG4, GOL
5	346	0.63	0.79	46	HT5, PG4

Interfaces

5 interfaces between chains.

A–B · 458 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 252 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 227 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 150 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 129 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (carboxylation).

Compared structures

4KF1 · Crystal structure of SsoPox W263I in complex with C10HTL · 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 4KF1 · PDBe 4KF1 · UniProt Q97VT7

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