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Human DNA polymerase iota incorporating dctp opposite 8-oxo-guanine

Analyse Human DNA polymerase iota incorporating dctp opposite 8-oxo-guanine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3Q8P
Type: protein + DNA
Length: 395 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase iota; DNA (5'-D(*TP*CP*AP*(8OG)P*GP*GP*GP*TP*CP*CP*T)-3'); DNA…
EC: 2.7.7.7
UniProt: Q9UNA4
Ligands: DCP, MG
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA polymerase iota (EC 2.7.7.7)	protein	380	46% helix, 21% strand	Q9UNA4
T	DNA (5'-D(TPCPAP(8OG)PGPGPGPTPCPCP*T)-3')	dna	8	—	—
P	DNA (5'-D(PAPGPGPAPCPCP*C)-3')	dna	7	—	—

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains B, T, P
MG · Magnesium ion · metal · 2 copies · chains B, P

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	618	0.73	0.80	45	empty
2	468	0.68	0.80	34	empty
3	386	0.68	0.81	38	DCP, MG
4	130	0.43	0.76	18	empty
5	70	0.29	0.73	15	empty

Interfaces

3 interfaces between chains.

B–T · 749 Å² buried · 16 hydrogen bonds · protein-nucleic
B–P · 524 Å² buried · 10 hydrogen bonds · protein-nucleic
T–P · 326 Å² buried · 28 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

3Q8P · Human DNA polymerase iota incorporating dCTP opposite 8-oxo-guanine · the same entry in another collection · chain B against B, TM-score 1.00
Q9UNA4 · AlphaFold monomer V2.0 prediction for DNA polymerase iota (Q9UNA4) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q9UNA4
Elsewhere: RCSB PDB 3Q8P · PDBe 3Q8P · UniProt Q9UNA4

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