MolNFT v2 · #25961 · protein

DNA polymerase from bacteriophage RB69

1WAJ: “DNA polymerase from bacteriophage RB69”. X-ray diffraction at 2.8, 1 ligand (5GP), 9 pockets (best druggability 0.77). MolNFT v2 #25961 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1WAJ
Type: protein
Length: 903 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.8
Source: Enterobacteria phage RB69
Molecule: DNA polymerase
EC: 2.7.7.7
UniProt: Q38087
Ligands: 5GP
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · resolution 2.8 · 1 distinct chain · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase (EC 2.7.7.7)	protein	903	42% helix, 16% strand	Q38087

Ligands and binding sites

5GP · Guanosine-5'-monophosphate · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	976	0.77	0.79	79	empty
2	480	0.63	0.76	45	empty
3	119	0.61	0.86	19	5GP
4	165	0.53	0.79	26	empty
5	142	0.50	0.79	22	empty

Compared structures

1WAJ · DNA polymerase from bacteriophage RB69 · 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 Q38087
Elsewhere: RCSB PDB 1WAJ · PDBe 1WAJ · UniProt Q38087

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