MolNFT v1 · #59171 · protein + DNA

Pre-insertion binary complex of dbh DNA polymerase

3BQ0 · DNA polymerase IV: “Pre-insertion binary complex of dbh DNA polymerase”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.78). MolNFT v1 #59171 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3BQ0
Type: protein + DNA
Length: 364 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DG)-3'); DNA (5'…
EC: 2.7.7.7
UniProt: Q4JB80
Ligands: CA
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase IV (EC 2.7.7.7)	protein	341	41% helix, 25% strand	Q4JB80
P	DNA (5'-D(DGPDAPDAPDGPDCPDCPDGPDGPDCPDG)-3')	dna	10	—	—
T	DNA (5'- D(DTDTPDCPDCPDGPDCPDCPDCPDGPDGPDCPDTPDTPDCP*DC)-3')	dna	13	—	—

Ligands and binding sites

CA · Calcium ion · metal · chains A, P

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 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	1055	0.78	0.80	71	CA
2	498	0.62	0.76	33	empty
3	143	0.55	0.81	17	empty
4	55	0.31	0.76	14	empty

Interfaces

3 interfaces between chains.

P–T · 471 Å² buried · 56 hydrogen bonds · nucleic-nucleic
A–T · 399 Å² buried · 4 hydrogen bonds · protein-nucleic
A–P · 346 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

3BQ0 · Pre-insertion binary complex of Dbh DNA polymerase · the same entry in another collection · chain A against A, TM-score 1.00
Q4JB80 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q4JB80) · a predicted model of the same protein · chain A against A, TM-score 0.78

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 Q4JB80
Elsewhere: RCSB PDB 3BQ0 · PDBe 3BQ0 · UniProt Q4JB80

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