MolNFT v1 · #135753 · protein + DNA

DNA polymerase beta crystallized in peg 400

5U8G: “DNA polymerase beta crystallized in peg 400”. X-ray diffraction, 2 ligands (NA, CL), 3 pockets (best druggability 0.72). MolNFT v1 #135753 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5U8G
Type: protein + DNA
Length: 346 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase beta; DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
EC: 2.7.7.7, 4.2.99.-
UniProt: P06746
Ligands: NA, CL
Pockets: 3 · best druggability 0.72

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase beta (EC 2.7.7.7, 4.2.99.-)	protein	315	51% helix, 13% strand	P06746
T	DNA (5'-D(CPCPGPAPCPAPGPCPGPCPAPTPCPAPGPC)- 3')	dna	16	—	—
P	DNA (5'-D(GPCPTPGPAPTPGPCPGPC)-3')	dna	10	—	—
D	DNA (5'-D(GPTPCPGP*G)-3')	dna	5	—	—

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, D, P
CL · Chloride ion · ion · 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	868	0.72	0.77	70	empty
2	184	0.61	0.83	24	empty
3	102	0.37	0.76	14	empty

Interfaces

5 interfaces between chains.

T–P · 474 Å² buried · 47 hydrogen bonds · nucleic-nucleic
A–T · 432 Å² buried · 10 hydrogen bonds · protein-nucleic
A–P · 366 Å² buried · 9 hydrogen bonds · protein-nucleic
A–D · 333 Å² buried · 6 hydrogen bonds · protein-nucleic
T–D · 228 Å² buried · 23 hydrogen bonds · nucleic-nucleic

Compared structures

5U8G · DNA Polymerase Beta crystallized in PEG 400 · 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 5U8G · PDBe 5U8G · UniProt P06746

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