MolNFT v1 · #136035 · protein + DNA

DNA polymerase beta nick complex with imidodiphosphate

5UGO: “DNA polymerase beta nick complex with imidodiphosphate”. X-ray diffraction, 2 ligands (2PN, CA). MolNFT v1 #136035 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5UGO
Type: protein + DNA
Length: 358 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: P06746
Ligands: 2PN, CA

Structure

x-ray diffraction · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	—	dna	16	—	—
P	—	dna	11	—	—
D	—	dna	5	—	—
A	—	protein	326	—	P06746

Ligands and binding sites

2PN · Imidodiphosphoric acid · ligand · chains P, A
CA · Calcium ion · metal · 2 copies · chains P, A

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

Compared structures

5UGO · DNA polymerase beta nick complex with imidodiphosphate · 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 0.95

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 5UGO · PDBe 5UGO · UniProt P06746

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