MolNFT v1 · #136036 · protein + DNA

DNA polymerase beta complex with a 1NT gap and dcmppnp

5UGP: “DNA polymerase beta complex with a 1NT gap and dcmppnp”. X-ray diffraction, 2 ligands (8CP, MG), 3 pockets (best druggability 0.71). MolNFT v1 #136036 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5UGP
Type: protein + DNA
Length: 354 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase beta; DNA (5'-D(P*GP*TP*CP*GP*G)-3'); DNA…
EC: 2.7.7.7, 4.2.99.-
UniProt: P06746
Ligands: 8CP, MG
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, 4.2.99.-)	protein	323	52% helix, 14% strand	P06746
D	DNA (5'-D(PGPTPCPGP*G)-3')	dna	5	—	—
P	DNA (5'-D(GPCPTPGPAPTPGPCPGPC)-3')	dna	10	—	—
T	DNA (5'-D(CPCPGPAPCPGPGPCPGPCPAPTPCPAPGPC)- 3')	dna	16	—	—

Ligands and binding sites

8CP · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonoamino) phosphoryl]oxy}phosphoryl]cytidine · ligand · chains A, P, T
MG · Magnesium ion · metal · 2 copies · chains A, P

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	999	0.71	0.76	61	8CP, MG
2	315	0.61	0.79	29	empty
3	219	0.58	0.80	28	empty

Interfaces

5 interfaces between chains.

A–T · 722 Å² buried · 15 hydrogen bonds · protein-nucleic
P–T · 469 Å² buried · 45 hydrogen bonds · nucleic-nucleic
A–D · 387 Å² buried · 10 hydrogen bonds · protein-nucleic
A–P · 366 Å² buried · 9 hydrogen bonds · protein-nucleic
D–T · 232 Å² buried · 21 hydrogen bonds · nucleic-nucleic

Compared structures

5UGP · DNA polymerase beta complex with a 1nt gap and dCMPPNP · 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 5UGP · PDBe 5UGP · UniProt P06746

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