MolNFT v1 · #186357 · protein + DNA

Human DNA polymerase beta crosslinked binary complex - B

7RBF · DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)…: “Human DNA polymerase beta crosslinked binary complex - B”. X-ray diffraction, 2 ligands (QPJ, NA), 2 pockets (best druggability 0.74). MolNFT v1 #186357 on GenesisL1: 3D…

PDB: 7RBF
Type: protein + DNA
Length: 355 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
EC: 2.7.7.7, 4.2.99.-
UniProt: P06746
Ligands: QPJ, NA
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	DNA (5'-D(CPCPGPAPCPGPGPCPGPCPAPTPCPAPGPC)- 3')	dna	16	—	—
P	DNA (5'-D(GPCPTPGPAPTPGPCPGPC)-3')	dna	10	—	—
D	DNA (5'-D(GPTPCPGP*G)-3')	dna	5	—	—
A	DNA polymerase beta (EC 2.7.7.7, 4.2.99.-)	protein	324	51% helix, 13% strand	P06746

Ligands and binding sites

QPJ · 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol · ligand · chains D, A
NA · Sodium ion · metal · 2 copies · chains P, A, D
EDO · 1,2-ethanediol · additive · 3 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A

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	1080	0.74	0.77	94	PEG
2	217	0.59	0.81	26	empty

Interfaces

5 interfaces between chains.

T–P · 469 Å² buried · 39 hydrogen bonds · nucleic-nucleic
T–A · 449 Å² buried · 10 hydrogen bonds · protein-nucleic
P–A · 349 Å² buried · 11 hydrogen bonds · protein-nucleic
D–A · 329 Å² buried · 5 hydrogen bonds · protein-nucleic
T–D · 228 Å² buried · 17 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7RBF · Human DNA polymerase beta crosslinked binary complex - B · the same entry in another collection · chain T against T, 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 0.93

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 7RBF · PDBe 7RBF · UniProt P06746

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