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Histidinol phosphate phosphatase from mycobacterium tuberculosis

Analyse Histidinol phosphate phosphatase from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZON
Type: protein
Length: 1,006 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histidinol-phosphatase
EC: 3.1.3.15
UniProt: P95189
Ligands: ZN, PO4
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Histidinol-phosphatase (EC 3.1.3.15)	protein	256	38% helix, 25% strand	P95189
B	Histidinol-phosphatase (EC 3.1.3.15)	protein	247	38% helix, 26% strand	P95189
D	Histidinol-phosphatase (EC 3.1.3.15)	protein	247	38% helix, 26% strand	P95189

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	99	0.76	0.96	24	empty
2	89	0.74	0.96	25	empty
3	402	0.66	0.80	47	GOL
4	242	0.56	0.78	30	empty
5	231	0.52	0.76	34	empty

Interfaces

3 interfaces between chains.

A–B · 1906 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 1891 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 593 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5ZON · Histidinol phosphate phosphatase from Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
P95189 · AlphaFold monomer V2.0 prediction for histidinol-phosphatase (P95189) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P95189
Elsewhere: RCSB PDB 5ZON · PDBe 5ZON · UniProt P95189

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