Research workbench

T-3 ternary complex of DPO4

Analyse T-3 ternary complex of DPO4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QZ7
Type: protein + DNA
Length: 369 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: Q97W02
Ligands: DCP, CA
Pockets: 3 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase IV (EC 2.7.7.7)	protein	341	45% helix, 25% strand	Q97W02
P	5'-D(GPGPCPAPCPTPGPAPTPCPGPGP*G)-3'	dna	13	—	—
T	5'-D(TPTPAPCPGPCPCPTPCPGPAPTPCPAPGPTPGPCP *C)-3'	dna	15	—	—

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, P, T
CA · Calcium ion · metal · 3 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1167	0.80	0.81	76	DCP, CA
2	548	0.73	0.81	40	empty
3	168	0.46	0.76	19	empty

Interfaces

3 interfaces between chains.

A–T · 917 Å² buried · 16 hydrogen bonds · protein-nucleic
P–T · 611 Å² buried · 52 hydrogen bonds · nucleic-nucleic
A–P · 567 Å² buried · 18 hydrogen bonds · protein-nucleic

Compared structures

3QZ7 · T-3 ternary complex of Dpo4 · the same entry in another collection · chain A against A, TM-score 1.00
Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · 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 Q97W02
Elsewhere: RCSB PDB 3QZ7 · PDBe 3QZ7 · UniProt Q97W02

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