MolNFT v1 · #97663 · protein + DNA

DNA polymerase beta matched nick complex with MG2+ and ppi, 30 min

4KLO · 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3': “DNA polymerase beta matched nick complex with MG2+ and ppi, 30 min”. X-ray diffraction, 3 ligands (PPV, NA, MG), 3 pockets (best druggability 0.70). MolNFT v1 #97663 on…

PDB: 4KLO
Type: protein + DNA
Length: 358 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'…
EC: 2.7.7.7, 4.2.99.-
UniProt: P06746
Ligands: PPV, NA, MG
Pockets: 3 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	5'-D(CPCPGPAPCPGPGPCPGPCPAPTPCPAPGPC)-3'	dna	16	—	—
P	5'-D(GPCPTPGPAPTPGPCPGPCP*C)-3'	dna	11	—	—
D	5'-D(PGPTPCPGP*G)-3'	dna	5	—	—
A	DNA polymerase beta (EC 2.7.7.7, 4.2.99.-)	protein	326	51% helix, 13% strand	P06746

Ligands and binding sites

PPV · Pyrophosphate · ligand · chains P, A
NA · Sodium ion · metal · 3 copies · chains P, A, D
MG · Magnesium ion · metal · 2 copies · chains P, A

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	895	0.70	0.76	63	MG, PPV
2	324	0.62	0.79	29	empty
3	225	0.57	0.79	26	empty

Interfaces

5 interfaces between chains.

T–A · 735 Å² buried · 16 hydrogen bonds · protein-nucleic
P–A · 535 Å² buried · 14 hydrogen bonds · protein-nucleic
T–P · 507 Å² buried · 45 hydrogen bonds · nucleic-nucleic
D–A · 390 Å² buried · 9 hydrogen bonds · protein-nucleic
T–D · 232 Å² buried · 17 hydrogen bonds · nucleic-nucleic

Compared structures

4KLO · DNA polymerase beta matched nick complex with Mg2+ and PPi, 30 min · 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 0.94

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 4KLO · PDBe 4KLO · UniProt P06746

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