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Nucleoside diphosphate kinase from aspergillus fumgiatus AF293 bound to udp

Analyse Nucleoside diphosphate kinase from aspergillus fumgiatus AF293 bound to udp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XPT
Type: protein
Length: 923 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase
EC: 2.7.4.6
UniProt: Q7Z8P9
Ligands: UDP, MG
Pockets: 14 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	153	47% helix, 16% strand	Q7Z8P9
B	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	155	47% helix, 15% strand	Q7Z8P9
C, E, G	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	154	47% helix, 16% strand	Q7Z8P9

Ligands and binding sites

UDP · Uridine-5'-diphosphate · ligand · 6 copies · chains A, B, E, C, G, H
MG · Magnesium ion · metal · 2 copies · chains B, G

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

Pockets

14 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	359	0.81	0.91	51	empty
2	364	0.81	0.90	50	empty
3	390	0.80	0.89	50	empty
4	215	0.65	0.84	35	empty
5	201	0.62	0.82	26	empty

Interfaces

12 interfaces between chains.

A–B · 987 Å² buried · 13 hydrogen bonds · protein-protein
C–H · 982 Å² buried · 13 hydrogen bonds · protein-protein
E–G · 978 Å² buried · 12 hydrogen bonds · protein-protein
B–E · 851 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 849 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6XPT · Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to UDP · the same entry in another collection · chain H against H, TM-score 1.00
Q7Z8P9 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (Q7Z8P9) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q7Z8P9
Elsewhere: RCSB PDB 6XPT · PDBe 6XPT · UniProt Q7Z8P9

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