Research workbench

DNA polymerase from bacteriophage RB69

Analyse DNA polymerase from bacteriophage RB69 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1WAF
Type: protein
Length: 1,806 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase
EC: 2.7.7.7
UniProt: Q38087
Ligands: GMP
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA polymerase (EC 2.7.7.7)	protein	903	41% helix, 16% strand	Q38087

Ligands and binding sites

GMP · Guanosine · ligand · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1109	0.81	0.83	101	empty
2	1019	0.78	0.80	83	empty
3	1059	0.77	0.79	77	empty
4	73	0.74	0.97	20	empty
5	55	0.73	0.98	18	empty

Interfaces

1 interface between chains.

A–B · 1180 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

1WAF · 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 1WAF · PDBe 1WAF · UniProt Q38087

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