MolNFT v1 · #161139 · protein + DNA

Klentaq DNA polymerase in complex with datp

6Q4V · DNA polymerase I, thermostable: “Klentaq DNA polymerase in complex with datp”. X-ray diffraction, 3 ligands (DTP, MG, MN), 8 pockets (best druggability 0.73). MolNFT v1 #161139 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6Q4V
Type: protein + DNA
Length: 566 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase I, thermostable; DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*(DOC))-3')…
EC: 2.7.7.7
UniProt: P19821
Ligands: DTP, MG, MN
Pockets: 8 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase I, thermostable (EC 2.7.7.7)	protein	538	53% helix, 13% strand	P19821
B	DNA (5'-D(GPAPCPCPAPCPGPGPCPCPAP(DOC))-3')	dna	12	—	—
C	DNA (5'-D(APAPCPTPGPTPGPGPCPCPGPTPGPGPTPC)- 3')	dna	16	—	—

Ligands and binding sites

DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, B, C
MG · Magnesium ion · metal · chains A, B
MN · Manganese (II) ion · metal · chains A
EDO · 1,2-ethanediol · additive · chains B, C

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

Pockets

8 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	428	0.73	0.83	42	DTP, MG, MN
2	993	0.72	0.76	45	empty
3	243	0.71	0.87	27	empty
4	293	0.60	0.79	34	empty
5	110	0.54	0.82	18	empty

Interfaces

3 interfaces between chains.

A–C · 1404 Å² buried · 25 hydrogen bonds · protein-nucleic
A–B · 827 Å² buried · 23 hydrogen bonds · protein-nucleic
B–C · 564 Å² buried · 50 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

6Q4V · KlenTaq DNA polymerase in complex with dATP · 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 6Q4V · PDBe 6Q4V · UniProt P19821

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