MolNFT v1 · #124611 · protein

Crystal structure of nucleoside diphosphate kinase from schistosoma mansoni in complex with ADP

5KK8: “Crystal structure of nucleoside diphosphate kinase from schistosoma mansoni in complex with ADP”. X-ray diffraction, 1 ligand (ADP), 3 pockets (best druggability 0.70). MolNFT v1 #124611 on GenesisL1: 3D structure, binding sites and…

PDB: 5KK8
Type: protein
Length: 298 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: G4VJY9
Ligands: ADP
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nucleoside diphosphate kinase (EC 2.7.4.6)	protein	149	46% helix, 16% strand	G4VJY9

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B

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

Pockets

3 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	792	0.70	0.76	71	ADP
2	51	0.30	0.76	14	empty
3	56	0.28	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 321 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5KK8 · Crystal structure of Nucleoside Diphosphate Kinase from Schistosoma mansoni in complex… · 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 G4VJY9
Elsewhere: RCSB PDB 5KK8 · PDBe 5KK8 · UniProt G4VJY9

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