MolNFT v1 · #99642 · protein + DNA

DNA polymerase beta E295K soaked with dumpnpp

4M9J: “DNA polymerase beta E295K soaked with dumpnpp”. X-ray diffraction, 4 ligands (DUP, NA, MG), 3 pockets (best druggability 0.72). MolNFT v1 #99642 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4M9J
Type: protein + DNA
Length: 338 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase beta; DNA template strand; DNA primer strand; DNA downstream strand
EC: 2.7.7.7, 4.2.99.-
UniProt: P06746
Ligands: DUP, NA, MG, CL
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase beta (EC 2.7.7.7, 4.2.99.-)	protein	307	52% helix, 12% strand	P06746
T	DNA template strand	dna	16	—	—
P	DNA primer strand	dna	10	—	—
D	DNA downstream strand	dna	5	—	—

Ligands and binding sites

DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains A, T, P
NA · Sodium ion · metal · 2 copies · chains A, D, P
MG · Magnesium ion · metal · chains A
CL · Chloride ion · ion · 2 copies · chains 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	837	0.72	0.77	69	MG, DUP
2	255	0.62	0.81	27	empty
3	100	0.39	0.76	14	empty

Interfaces

5 interfaces between chains.

T–P · 472 Å² buried · 45 hydrogen bonds · nucleic-nucleic
A–T · 469 Å² buried · 10 hydrogen bonds · protein-nucleic
A–D · 328 Å² buried · 6 hydrogen bonds · protein-nucleic
A–P · 324 Å² buried · 8 hydrogen bonds · protein-nucleic
T–D · 232 Å² buried · 26 hydrogen bonds · nucleic-nucleic

Compared structures

4M9J · DNA Polymerase Beta E295K Soaked with dUMPNPP · 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 0.95

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 4M9J · PDBe 4M9J · UniProt P06746

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