MolNFT v1 · #73931 · protein + DNA

Yeast DNA polymerase eta extending from an 8-oxog lesion

3OHB: “Yeast DNA polymerase eta extending from an 8-oxog lesion”. X-ray diffraction, 3 ligands (DCP, MG, SO4), 3 pockets (best druggability 0.82). MolNFT v1 #73931 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3OHB
Type: protein + DNA
Length: 539 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase eta; 5'-D(*TP*AP*AP*TP*GP*(8OG)P*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)- 3'…
EC: 2.7.7.7
UniProt: Q04049
Ligands: DCP, MG, SO4
Pockets: 3 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase eta (EC 2.7.7.7)	protein	515	40% helix, 19% strand	Q04049
T	5'-D(TPAPAPTPGP(8OG)PAPGPGPGPGPAPGPGPAPC)- 3'	dna	13	—	—
P	5'-D(GPTPCPCPTPCPCPCPCPTP*(DOC))-3'	dna	11	—	—

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, T, P
MG · Magnesium ion · metal · 2 copies · chains A, P
SO4 · Sulfate ion · ion · 3 copies · chains A, P

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

Pockets

3 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	1101	0.82	0.84	89	DCP, MG
2	539	0.70	0.80	37	SO4
3	55	0.41	0.82	17	empty

Interfaces

3 interfaces between chains.

A–T · 716 Å² buried · 22 hydrogen bonds · protein-nucleic
A–P · 537 Å² buried · 8 hydrogen bonds · protein-nucleic
T–P · 506 Å² buried · 48 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

3OHB · Yeast DNA polymerase eta extending from an 8-oxoG lesion · the same entry in another collection · chain A against A, TM-score 1.00
Q04049 · AlphaFold monomer V2.0 prediction for DNA polymerase eta (Q04049) · a predicted model of the same protein · chain A 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 Q04049
Elsewhere: RCSB PDB 3OHB · PDBe 3OHB · UniProt Q04049

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