Research workbench

Y-family DNA polymerase chimera dbh-DPO4(243-245)-dbh

Analyse Y-family DNA polymerase chimera dbh-DPO4(243-245)-dbh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NLG
Type: protein + DNA
Length: 375 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; 5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*G)-3'…
EC: 2.7.7.7
UniProt: Q4JB80
Ligands: DCP, CA
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase IV (EC 2.7.7.7)	protein	344	41% helix, 26% strand	Q4JB80
P	5'-D(GPGPCPAPCPTPGPAPTPCPGPGP*G)-3'	dna	13	—	—
T	5'-D(TPTPAPCPGPCPCPCPTPGPAPTPCPAPGPTPGPCP *C)-3'	dna	18	—	—

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, P, T
CA · Calcium ion · metal · 2 copies · chains A, P

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1190	0.77	0.80	81	CA, DCP
2	400	0.66	0.79	37	empty

Interfaces

3 interfaces between chains.

A–T · 1089 Å² buried · 17 hydrogen bonds · protein-nucleic
P–T · 631 Å² buried · 59 hydrogen bonds · nucleic-nucleic
A–P · 514 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

4NLG · Y-family DNA polymerase chimera Dbh-Dpo4(243-245)-Dbh · 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 0.98

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 4NLG · PDBe 4NLG · UniProt Q4JB80

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