MolNFT v1 · #124925 · protein

Large fragment of taq DNA polymerase bound to dctp

5KTQ · Protein (DNA polymerase I): “Large fragment of taq DNA polymerase bound to dctp”. X-ray diffraction, 1 ligand (DCP), 4 pockets (best druggability 0.62). MolNFT v1 #124925 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5KTQ
Type: protein
Length: 534 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (DNA polymerase I)
EC: 2.7.7.7
UniProt: P19821
Ligands: DCP
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein (DNA polymerase I) (EC 2.7.7.7)	protein	534	51% helix, 13% strand	P19821

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	250	0.62	0.81	35	empty
2	296	0.57	0.77	33	empty
3	121	0.43	0.76	20	empty
4	50	0.37	0.80	13	empty

Compared structures

5KTQ · Large fragment of taq DNA polymerase bound to dctp · the same entry in another collection · chain A against A, TM-score 1.00
P19821 · AlphaFold monomer V2.0 prediction for DNA polymerase I, thermostable (P19821) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P19821
Elsewhere: RCSB PDB 5KTQ · PDBe 5KTQ · UniProt P19821

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