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Crystal structure of nucleoside diphosphate kinase at 1.92 a resolution from acinetobacter baumannii

Analyse Crystal structure of nucleoside diphosphate kinase at 1.92 a resolution from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4S0M
Type: protein
Length: 1,144 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: V5VIC4
Ligands: MG
Pockets: 13 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, G, H, I	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	143	43% helix, 20% strand	V5VIC4

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains D, G

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

Pockets

13 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	1179	0.81	0.82	84	empty
2	1166	0.80	0.81	89	empty
3	433	0.58	0.74	40	empty
4	266	0.53	0.76	26	empty
5	180	0.51	0.78	24	empty

Interfaces

15 interfaces between chains.

H–I · 1258 Å² buried · 27 hydrogen bonds · protein-protein
F–G · 1252 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1221 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1210 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 423 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4S0M · Crystal Structure of nucleoside diphosphate kinase at 1.92 A resolution from… · 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 V5VIC4
Elsewhere: RCSB PDB 4S0M · PDBe 4S0M · UniProt V5VIC4

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