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Structure of a HAM1 protein from coxiella burnetii

Analyse Structure of a HAM1 protein from coxiella burnetii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TQU
Type: protein
Length: 788 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Non-canonical purine ntp pyrophosphatase
EC: 3.6.1.19
UniProt: Q83FA3
Ligands: CA
Pockets: 7 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Non-canonical purine ntp pyrophosphatase (EC 3.6.1.19)	protein	197	39% helix, 24% strand	Q83FA3

Ligands and binding sites

CA · Calcium ion · metal · 5 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · chains 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	428	0.63	0.77	53	CA, EDO
2	353	0.63	0.79	50	CA
3	322	0.62	0.79	36	CA
4	347	0.62	0.78	46	CA
5	469	0.58	0.74	68	empty

Interfaces

3 interfaces between chains.

C–D · 869 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 844 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 422 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

3TQU · Structure of a HAM1 protein from Coxiella burnetii · the same entry in another collection · chain A against A, TM-score 1.00
Q83FA3 · AlphaFold monomer V2.0 prediction for DITP/XTP pyrophosphatase (Q83FA3) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q83FA3
Elsewhere: RCSB PDB 3TQU · PDBe 3TQU · UniProt Q83FA3

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