MolNFT v1 · #91096 · protein

Crystal structure of nucleoside diphosphate kinase B from trypanosoma brucei, apo form

4F36: “Crystal structure of nucleoside diphosphate kinase B from trypanosoma brucei, apo form”. X-ray diffraction, 1 ligand (SCN), 17 pockets (best druggability 0.83). MolNFT v1 #91096 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4F36
Type: protein
Length: 842 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: Q381H3
Ligands: SCN
Pockets: 17 · best druggability 0.83

Structure

x-ray diffraction · 6 distinct chains · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	141	46% helix, 18% strand	Q381H3
C	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	140	44% helix, 19% strand	Q381H3
B	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	140	44% helix, 19% strand	Q381H3
D	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	138	43% helix, 19% strand	Q381H3
E	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	147	44% helix, 18% strand	Q381H3
F	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	136	45% helix, 19% strand	Q381H3

Ligands and binding sites

SCN · Thiocyanate ion · ion · chains F

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

Pockets

17 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	431	0.83	0.91	75	empty
2	277	0.81	0.92	52	empty
3	217	0.79	0.93	39	empty
4	126	0.67	0.89	27	empty
5	64	0.54	0.87	22	empty

Interfaces

15 interfaces between chains.

E–F · 1181 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 1178 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1154 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 728 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 714 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4F36 · Crystal structure of Nucleoside diphosphate kinase B from Trypanosoma brucei, apo form · 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 Q381H3
Elsewhere: RCSB PDB 4F36 · PDBe 4F36 · UniProt Q381H3

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