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Crystal structure of staphylococcus aureus nucleoside diphosphate kinase complexed with cdp

Analyse Crystal structure of staphylococcus aureus nucleoside diphosphate kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3Q89
Type: protein
Length: 1,192 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase
EC: 2.7.4.6
UniProt: Q5HFV4
Ligands: CDP, MG
Pockets: 12 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	149	45% helix, 17% strand	Q5HFV4

Ligands and binding sites

CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains B, E
MG · Magnesium ion · metal · 2 copies · chains B, E

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

Pockets

12 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	1147	0.87	0.88	90	empty
2	1008	0.80	0.82	99	empty
3	257	0.63	0.81	29	empty
4	549	0.62	0.75	70	empty
5	188	0.52	0.78	29	MG, CDP

Interfaces

19 interfaces between chains.

A–D · 1067 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1061 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1057 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 945 Å² buried · 13 hydrogen bonds · protein-protein
C–F · 918 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3Q89 · Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with… · the same entry in another collection · chain H against H, TM-score 1.00
Q5HFV4 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase (Q5HFV4) · 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 Q5HFV4
Elsewhere: RCSB PDB 3Q89 · PDBe 3Q89 · UniProt Q5HFV4

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