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X-ray structure of NM23 human nucleoside diphosphate kinase B complexed with GDP at 2 ångströms resolution

Analyse X-ray structure of NM23 human nucleoside diphosphate kinase B complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NUE
Type: protein
Length: 906 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: P22392
Ligands: GDP, MG
Pockets: 15 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	151	48% helix, 16% strand	P22392

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, F, E
MG · Magnesium ion · metal · 2 copies · chains A, C

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

Pockets

15 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	818	0.87	0.90	89	empty
2	475	0.85	0.92	55	empty
3	508	0.85	0.91	57	empty
4	300	0.77	0.89	39	empty
5	205	0.51	0.77	29	GDP

Interfaces

12 interfaces between chains.

A–D · 1051 Å² buried · 14 hydrogen bonds · protein-protein
B–E · 1048 Å² buried · 16 hydrogen bonds · protein-protein
C–F · 1044 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 830 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 817 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1NUE · X-ray structure of NM23 human nucleoside diphosphate kinase B complexed with GDP at 2… · the same entry in another collection · chain C against C, TM-score 1.00
P22392 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase B (P22392) · 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 P22392
Elsewhere: RCSB PDB 1NUE · PDBe 1NUE · UniProt P22392

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