MolNFT v1 · #115358 · protein

Gkap mutant B12

5CH9 · Phosphotriesterase: “Gkap mutant B12”. X-ray diffraction, 1 ligand (CO), 7 pockets (best druggability 0.76). MolNFT v1 #115358 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5CH9
Type: protein
Length: 656 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphotriesterase
EC: 3.5.-.-
UniProt: Q5KZU5
Ligands: CO
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phosphotriesterase (EC 3.5.-.-)	protein	328	45% helix, 17% strand	Q5KZU5

Ligands and binding sites

CO · Cobalt (II) ion · metal · 4 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	333	0.76	0.87	47	empty
2	289	0.76	0.88	47	empty
3	93	0.72	0.95	27	empty
4	781	0.68	0.75	70	empty
5	198	0.46	0.74	30	empty

Interfaces

1 interface between chains.

A–B · 1915 Å² buried · 41 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (carboxylation).

Compared structures

5CH9 · Gkap mutant B12 · the same entry in another collection · 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 Q5KZU5
Elsewhere: RCSB PDB 5CH9 · PDBe 5CH9 · UniProt Q5KZU5

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