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R80N mutant of nucleoside diphosphate kinase from mycobacterium tuberculosis

Analyse R80N mutant of nucleoside diphosphate kinase from mycobacterium tuberculosis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ANE
Type: protein
Length: 795 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: P84284
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	135	45% helix, 18% strand	P84284
B	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	132	42% helix, 20% strand	P84284
D	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	131	41% helix, 20% strand	P84284
F	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	127	39% helix, 19% strand	P84284

Ligands and binding sites

CIT · Citric acid · additive · 3 copies · chains A, D, F

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	700	0.81	0.85	68	empty
2	146	0.51	0.79	26	CIT
3	157	0.51	0.79	26	empty
4	141	0.50	0.79	25	empty
5	122	0.44	0.77	25	empty

Interfaces

11 interfaces between chains.

A–B · 673 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 672 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 657 Å² buried · 17 hydrogen bonds · protein-protein
A–E · 571 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 563 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4ANE · R80N mutant of nucleoside diphosphate kinase from mycobacterium tuberculosis · 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 P84284
Elsewhere: RCSB PDB 4ANE · PDBe 4ANE · UniProt P84284

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