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Crystal structure of the sphingobium sp. TCM1 phosphotriesterase without the binuclear manganese center

Analyse Crystal structure of the sphingobium sp. TCM1 phosphotriesterase without the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IOJ
Type: protein
Length: 989 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Haloalkylphosphorus hydrolase
UniProt: A0A077JBW9
Pockets: 8 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Haloalkylphosphorus hydrolase	protein	494	9% helix, 36% strand	A0A077JBW9
B	Haloalkylphosphorus hydrolase	protein	495	9% helix, 36% strand	A0A077JBW9

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1105	0.85	0.86	103	empty
2	86	0.77	0.98	24	empty
3	85	0.77	0.98	24	empty
4	575	0.72	0.80	44	empty
5	534	0.71	0.80	46	empty

Interfaces

1 interface between chains.

A–B · 2301 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5IOJ · Crystal structure of the Sphingobium sp. TCM1 phosphotriesterase without the binuclear… · 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 A0A077JBW9
Elsewhere: RCSB PDB 5IOJ · PDBe 5IOJ · UniProt A0A077JBW9

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