MolNFT v1 · #92987 · protein

Polynucleotide kinase

4GP6 · Metallophosphoesterase: “Polynucleotide kinase”. X-ray diffraction, 2 ligands (ADP, MG), 5 pockets (best druggability 0.60). MolNFT v1 #92987 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GP6
Type: protein
Length: 341 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: ADP, MG
Pockets: 5 · best druggability 0.60

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Metallophosphoesterase (EC 2.7.1.78)	protein	171	52% helix, 20% strand	A3DJ38
B	Metallophosphoesterase (EC 2.7.1.78)	protein	170	50% helix, 19% strand	A3DJ38

Ligands and binding sites

ADP · Adenosine-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

5 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	173	0.60	0.82	19	empty
2	266	0.59	0.79	36	ADP, MG
3	290	0.57	0.77	39	ADP, MG
4	72	0.39	0.79	17	empty
5	57	0.31	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 846 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4GP6 · 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 4GP6 · PDBe 4GP6 · UniProt A3DJ38

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