MolNFT v1 · #92988 · protein

Polynucleotide kinase

4GP7 · Metallophosphoesterase: “Polynucleotide kinase”. X-ray diffraction, 3 ligands (ATP, MG, NA), 4 pockets (best druggability 0.63). MolNFT v1 #92988 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GP7
Type: protein
Length: 342 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metallophosphoesterase
EC: 2.7.1.78
UniProt: A3DJ38
Ligands: ATP, MG, NA
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Metallophosphoesterase (EC 2.7.1.78)	protein	171	50% helix, 22% strand	A3DJ38

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · chains B
CIT · Citric acid · additive · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	446	0.63	0.77	47	ATP, MG
2	188	0.62	0.83	18	CIT
3	248	0.54	0.77	37	ATP, MG
4	80	0.40	0.78	14	empty

Interfaces

1 interface between chains.

A–B · 891 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

4GP7 · Polynucleotide 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 A3DJ38
Elsewhere: RCSB PDB 4GP7 · PDBe 4GP7 · UniProt A3DJ38

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