MolNFT v1 · #179555 · protein + DNA

Human DNA polymerase beta dgdp product complex with MN2+

7K97: “Human DNA polymerase beta dgdp product complex with MN2+”. X-ray diffraction, 3 ligands (MN, NA, PO4), 2 pockets (best druggability 0.72). MolNFT v1 #179555 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7K97
Type: protein + DNA
Length: 358 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase beta; DNA (5'-D(P*GP*TP*CP*GP*G)-3'); DNA…
EC: 2.7.7.7, 4.2.99.-
UniProt: P06746
Ligands: MN, NA, PO4
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase beta (EC 2.7.7.7, 4.2.99.-)	protein	326	50% helix, 13% strand	P06746
D	DNA (5'-D(PGPTPCPGP*G)-3')	dna	5	—	—
P	DNA (5'-D(GPCPTPGPAPTPGPCPGPCP*G)-3')	dna	11	—	—
T	DNA (5'-D(CPCPGPAPCPCPGPCPGPCPAPTPCPAPGPC)- 3')	dna	16	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 8 copies · chains A, P, T, D
NA · Sodium ion · metal · 2 copies · chains A, P, D
PO4 · Phosphate ion · ion · chains A, P

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

Pockets

2 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	1177	0.72	0.76	79	NA, MN, PO4
2	296	0.63	0.80	29	empty

Interfaces

5 interfaces between chains.

A–T · 736 Å² buried · 16 hydrogen bonds · protein-nucleic
A–P · 564 Å² buried · 18 hydrogen bonds · protein-nucleic
P–T · 529 Å² buried · 47 hydrogen bonds · nucleic-nucleic
A–D · 380 Å² buried · 13 hydrogen bonds · protein-nucleic
D–T · 239 Å² buried · 26 hydrogen bonds · nucleic-nucleic

Compared structures

7K97 · Human DNA polymerase beta dGDP product complex with Mn2+ · the same entry in another collection · chain A against A, TM-score 1.00
P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P06746
Elsewhere: RCSB PDB 7K97 · PDBe 7K97 · UniProt P06746

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.