MolNFT v1 · #12022 · protein

Mycobacterium tuberculosis nucleoside diphosphate kinase

1K44: “Mycobacterium tuberculosis nucleoside diphosphate kinase”. X-ray diffraction, 13 pockets (best druggability 0.81). MolNFT v1 #12022 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1K44
Type: protein
Length: 810 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: 13 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	135	42% helix, 19% strand	P84284

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	717	0.81	0.86	61	empty
2	185	0.49	0.76	30	empty
3	175	0.48	0.76	23	empty
4	182	0.48	0.76	23	empty
5	174	0.46	0.76	24	empty

Interfaces

12 interfaces between chains.

B–F · 618 Å² buried · 12 hydrogen bonds · protein-protein
C–E · 614 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 611 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 601 Å² buried · 12 hydrogen bonds · protein-protein
D–F · 599 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

1K44 · Mycobacterium tuberculosis Nucleoside Diphosphate Kinase · 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 1K44 · PDBe 1K44 · UniProt P84284

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