MolNFT v1 · #88253 · protein

Ndpk in complex with (rp)-spmpapp

4CP5 · Nucleoside diphosphate kinase, cytosolic: “Ndpk in complex with (rp)-spmpapp”. X-ray diffraction, 1 ligand (EOI), 16 pockets (best druggability 0.80). MolNFT v1 #88253 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4CP5
Type: protein
Length: 906 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase, cytosolic
EC: 2.7.4.6
UniProt: P22887
Ligands: EOI
Pockets: 16 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Nucleoside diphosphate kinase, cytosolic (EC 2.7.4.6)	protein	151	42% helix, 17% strand	P22887

Ligands and binding sites

EOI · [[(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-sulfanyl-phosphoryl] phosphono hydrogen phosphate · ligand · 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

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	634	0.80	0.85	69	empty
2	640	0.80	0.85	69	empty
3	384	0.77	0.86	55	empty
4	222	0.71	0.87	34	empty
5	194	0.70	0.87	33	empty

Interfaces

9 interfaces between chains.

E–F · 768 Å² buried · 8 hydrogen bonds · protein-protein
D–F · 761 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 760 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 760 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 760 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4CP5 · ndpK in complex with (Rp)-SPMPApp · the same entry in another collection · chain C against C, TM-score 1.00
P22887 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase, cytosolic (P22887) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P22887
Elsewhere: RCSB PDB 4CP5 · PDBe 4CP5 · UniProt P22887

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