MolNFT v1 · #61167 · protein

Crystal structure of the mimivirus ndk +kpn-N62L-R107G triple mutant complexed with tdp

3DDI · Nucleoside diphosphate kinase: “Crystal structure of the mimivirus ndk +kpn-N62L-R107G triple mutant complexed with tdp”. X-ray diffraction, 2 ligands (TYD, MG), 2 pockets (best druggability 0.45). MolNFT v1 #61167 on GenesisL1: 3D…

PDB: 3DDI
Type: protein
Length: 266 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase
EC: 2.7.4.6
UniProt: Q5UQL3
Ligands: TYD, MG
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	133	44% helix, 20% strand	Q5UQL3

Ligands and binding sites

TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	142	0.45	0.76	24	MG, TYD
2	127	0.44	0.77	23	MG, TYD

Interfaces

1 interface between chains.

A–B · 39 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3DDI · Crystal structure of the mimivirus NDK +Kpn-N62L-R107G triple mutant complexed with TDP · 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 3DDI · PDBe 3DDI · UniProt Q5UQL3

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