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Plasmodium falciparum nucleoside diphosphate kinase B

Analyse Plasmodium falciparum nucleoside diphosphate kinase B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1XIQ
Type: protein
Length: 894 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase B
EC: 2.7.4.6
UniProt: Q8ID43
Pockets: 15 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Nucleoside diphosphate kinase B (EC 2.7.4.6)	protein	149	42% helix, 17% strand	Q8ID43

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	961	0.86	0.87	64	empty
2	207	0.84	0.97	42	empty
3	199	0.84	0.97	41	empty
4	168	0.82	0.97	40	empty
5	361	0.63	0.78	41	empty

Interfaces

12 interfaces between chains.

B–E · 1102 Å² buried · 19 hydrogen bonds · protein-protein
A–F · 1091 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1074 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 948 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 933 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1XIQ · Plasmodium falciparum Nucleoside diphosphate kinase B · the same entry in another collection · chain E against E, 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 Q8ID43
Elsewhere: RCSB PDB 1XIQ · PDBe 1XIQ · UniProt Q8ID43

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