MolNFT v1 · #96875 · protein + DNA

Ternary complex of D256A mutant of DNA polymerase beta

4JWN: “Ternary complex of D256A mutant of DNA polymerase beta”. X-ray diffraction, 4 ligands (DUP, NA, MG), 3 pockets (best druggability 0.71). MolNFT v1 #96875 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4JWN
Type: protein + DNA
Length: 357 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
UniProt: P06746
Ligands: DUP, NA, MG, CL
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase beta (EC 2.7.7.7)	protein	326	52% helix, 14% strand	P06746
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	—	—

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, P, D
MG · Magnesium ion · metal · chains A
CL · Chloride ion · ion · 4 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	934	0.71	0.76	57	DUP, MG
2	362	0.63	0.79	32	empty
3	252	0.63	0.82	36	empty

Interfaces

5 interfaces between chains.

A–T · 735 Å² buried · 15 hydrogen bonds · protein-nucleic
T–P · 469 Å² buried · 43 hydrogen bonds · nucleic-nucleic
A–P · 393 Å² buried · 10 hydrogen bonds · protein-nucleic
A–D · 370 Å² buried · 11 hydrogen bonds · protein-nucleic
T–D · 229 Å² buried · 26 hydrogen bonds · nucleic-nucleic

Compared structures

4JWN · Ternary complex of D256A mutant of DNA Polymerase Beta · 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 4JWN · PDBe 4JWN · UniProt P06746

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