MolNFT v1 · #62642 · protein

X-ray structure of acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with dudp

3ELH: “X-ray structure of acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with dudp”. X-ray diffraction, 2 ligands (DUD, MG), 8 pockets (best druggability 0.64). MolNFT v1 #62642 on GenesisL1: 3D structure, binding…

PDB: 3ELH
Type: protein
Length: 789 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: Q5UQL3
Ligands: DUD, MG
Pockets: 8 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	133	44% helix, 21% strand	Q5UQL3
B	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	130	45% helix, 20% strand	Q5UQL3
C, D, E	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	132	43% helix, 21% strand	Q5UQL3
F	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	130	45% helix, 22% strand	Q5UQL3

Ligands and binding sites

DUD · Deoxyuridine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	304	0.64	0.80	33	empty
2	285	0.61	0.79	30	empty
3	139	0.43	0.76	25	DUD, MG
4	127	0.42	0.76	25	DUD, MG
5	125	0.42	0.76	22	DUD, MG

Interfaces

6 interfaces between chains.

A–C · 530 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 520 Å² buried · 10 hydrogen bonds · protein-protein
D–F · 520 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 518 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 517 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3ELH · X-ray structure of Acanthamoeba ployphaga mimivirus 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 Q5UQL3
Elsewhere: RCSB PDB 3ELH · PDBe 3ELH · UniProt Q5UQL3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.