MolNFT v1 · #185013 · protein

Vibriophage PHIVC8 family a DNA polymerase (dpoz), two conformations: thumb-exo open and thumb-exo closed

7PBK · DNA polymerase I: “Vibriophage PHIVC8 family a DNA polymerase (dpoz), two conformations: thumb-exo open and thumb-exo closed”. X-ray diffraction, 14 pockets (best druggability 0.72). MolNFT v1 #185013 on GenesisL1: 3D structure…

PDB: 7PBK
Type: protein
Length: 1,237 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase I
UniProt: G3FFN8
Pockets: 14 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase I	protein	624	51% helix, 15% strand	G3FFN8
B	DNA polymerase I	protein	613	50% helix, 14% strand	G3FFN8

Pockets

14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	724	0.72	0.78	69	empty
2	597	0.71	0.79	55	empty
3	132	0.64	0.87	18	empty
4	410	0.57	0.74	40	empty
5	207	0.50	0.76	26	empty

Interfaces

1 interface between chains.

A–B · 276 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7PBK · Vibriophage phiVC8 family A DNA polymerase (DpoZ), two conformations: thumb-exo open and… · 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 G3FFN8
Elsewhere: RCSB PDB 7PBK · PDBe 7PBK · UniProt G3FFN8

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