MolNFT v1 · #141707 · protein

Crystal structure of APRT2 from thermus thermophilus HB8

5ZGO · Adenine phosphoribosyltransferase: “Crystal structure of APRT2 from thermus thermophilus HB8”. X-ray diffraction, 15 pockets (best druggability 0.82). MolNFT v1 #141707 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZGO
Type: protein
Length: 1,068 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenine phosphoribosyltransferase
UniProt: Q5SHW6
Pockets: 15 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Adenine phosphoribosyltransferase	protein	178	24% helix, 34% strand	Q5SHW6

Pockets

15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	572	0.82	0.87	64	empty
2	1153	0.79	0.80	82	empty
3	478	0.75	0.83	38	empty
4	974	0.74	0.77	77	empty
5	180	0.69	0.87	28	empty

Interfaces

8 interfaces between chains.

C–D · 1146 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1035 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 960 Å² buried · 7 hydrogen bonds · protein-protein
C–E · 632 Å² buried · 2 hydrogen bonds · protein-protein
A–F · 482 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5ZGO · Crystal structure of APRT2 from Thermus thermophilus HB8 · 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 Q5SHW6
Elsewhere: RCSB PDB 5ZGO · PDBe 5ZGO · UniProt Q5SHW6

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