MolNFT v1 · #2217 · protein + DNA

Human DNA polymerase beta complexed with nicked DNA

1BPZ · DNA (5'- D(*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)…: “Human DNA polymerase beta complexed with nicked DNA”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.77). MolNFT v1 #2217 on GenesisL1: 3D structure…

PDB: 1BPZ
Type: protein + DNA
Length: 363 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); DNA…
EC: 2.7.7.7
UniProt: P06746
Ligands: NA
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	DNA (5'- D(CPCPGPAPCPCPAPCPGPCPAPTPCPAPGPC)-3')	dna	16	—	—
P	DNA (5'-D(GPCPTPGPAPTPGPCPGPTP*G)-3')	dna	11	—	—
D	DNA (5'-D(GPTPCPGP*G)-3')	dna	5	—	—
A	Protein (DNA polymerase beta) (EC 2.7.7.7)	protein	331	51% helix, 11% strand	P06746

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains P, A, D

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

Pockets

3 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	435	0.77	0.86	46	empty
2	555	0.62	0.75	40	empty
3	304	0.52	0.74	31	empty

Interfaces

5 interfaces between chains.

T–P · 504 Å² buried · 50 hydrogen bonds · nucleic-nucleic
T–A · 466 Å² buried · 16 hydrogen bonds · protein-nucleic
P–A · 464 Å² buried · 19 hydrogen bonds · protein-nucleic
D–A · 373 Å² buried · 12 hydrogen bonds · protein-nucleic
T–D · 235 Å² buried · 26 hydrogen bonds · nucleic-nucleic

Compared structures

1BPZ · Human DNA polymerase beta complexed with nicked DNA · 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 0.92

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 1BPZ · PDBe 1BPZ · UniProt P06746

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