MolNFT v1 · #138592 · protein + DNA

DNA polymerase beta substrate complex with incoming 5-fodutp

5WO0 · DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)…: “DNA polymerase beta substrate complex with incoming 5-fodutp”. X-ray diffraction, 4 ligands (B7A, NA, CA), 3 pockets (best druggability 0.71). MolNFT v1 #138592 on…

PDB: 5WO0
Type: protein + DNA
Length: 357 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 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: B7A, NA, CA, CL
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	DNA (5'-D(CPCPGPAPCPAPGPCPGPCPAPTPCPAPGPC)- 3')	dna	16	—	—
P	DNA (5'-D(GPCPTPGPAPTPGPCPGPC)-3')	dna	10	—	—
D	DNA (5'-D(PGPTPCPGP*G)-3')	dna	5	—	—
A	DNA polymerase beta (EC 2.7.7.7, 4.2.99.-)	protein	326	52% helix, 13% strand	P06746

Ligands and binding sites

B7A · 2'-deoxy-5-formyluridine 5'-(tetrahydrogen triphosphate) · ligand · chains T, P, A
NA · Sodium ion · metal · 2 copies · chains P, A, D
CA · Calcium ion · metal · 2 copies · chains P, A
CL · Chloride ion · ion · 3 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	970	0.71	0.76	63	B7A, CA
2	327	0.62	0.79	29	empty
3	217	0.57	0.80	28	empty

Interfaces

5 interfaces between chains.

T–A · 732 Å² buried · 12 hydrogen bonds · protein-nucleic
T–P · 470 Å² buried · 48 hydrogen bonds · nucleic-nucleic
D–A · 377 Å² buried · 9 hydrogen bonds · protein-nucleic
P–A · 374 Å² buried · 9 hydrogen bonds · protein-nucleic
T–D · 232 Å² buried · 19 hydrogen bonds · nucleic-nucleic

Compared structures

5WO0 · DNA polymerase beta substrate complex with incoming 5-FodUTP · 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 5WO0 · PDBe 5WO0 · UniProt P06746

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