MolNFT v1 · #27865 · protein

Bacillus stearothermophilus (newly identified strain as yet unnamed) DNA polymerase fragment

1XWL · DNA polymerase I: “Bacillus stearothermophilus (newly identified strain as yet unnamed) DNA polymerase fragment”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.66). MolNFT v1 #27865 on GenesisL1: 3D structure…

PDB: 1XWL
Type: protein
Length: 580 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase I
EC: 2.7.7.7
UniProt: P52026
Ligands: SO4
Pockets: 6 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 55% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase I (EC 2.7.7.7)	protein	580	55% helix, 13% strand	P52026

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	307	0.66	0.81	42	empty
2	141	0.46	0.77	25	empty
3	157	0.45	0.76	21	empty
4	152	0.43	0.74	21	empty
5	134	0.40	0.74	18	empty

Compared structures

1XWL · Bacillus stearothermophilus (newly identified strain as yet unnamed) DNA polymerase… · the same entry in another collection · chain A against A, TM-score 1.00
P52026 · AlphaFold monomer V2.0 prediction for DNA polymerase I (P52026) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P52026
Elsewhere: RCSB PDB 1XWL · PDBe 1XWL · UniProt P52026

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