MolNFT v1 · #138591 · protein + DNA

DNA polymerase beta substrate complex with incoming 5-fodctp

5WNZ · DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)…: “DNA polymerase beta substrate complex with incoming 5-fodctp”. X-ray diffraction, 4 ligands (B7J, NA, CA), 3 pockets (best druggability 0.70). MolNFT v1 #138591 on…

PDB: 5WNZ
Type: protein + DNA
Length: 356 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
EC: 2.7.7.7, 4.2.99.-
UniProt: P06746
Ligands: B7J, NA, CA, CL
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	DNA (5'-D(CPCPGPAPCPGPGPCPGPCPAPTPCPAPGPC)- 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	325	51% helix, 14% strand	P06746

Ligands and binding sites

B7J · 2'-deoxy-5-formylcytidine 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 A, 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	885	0.70	0.76	56	CA, B7J
2	347	0.62	0.78	29	empty
3	174	0.56	0.81	25	empty

Interfaces

5 interfaces between chains.

T–A · 731 Å² buried · 11 hydrogen bonds · protein-nucleic
T–P · 464 Å² buried · 42 hydrogen bonds · nucleic-nucleic
D–A · 379 Å² buried · 10 hydrogen bonds · protein-nucleic
P–A · 375 Å² buried · 9 hydrogen bonds · protein-nucleic
T–D · 234 Å² buried · 25 hydrogen bonds · nucleic-nucleic

Compared structures

5WNZ · DNA polymerase beta substrate complex with incoming 5-FodCTP · 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 5WNZ · PDBe 5WNZ · UniProt P06746

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