Research workbench

DNA polymerase IV - DNA ternary complex 6

Analyse DNA polymerase IV - DNA ternary complex 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YUW
Type: protein + DNA
Length: 749 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; DTN1; DTN2C
EC: 2.7.7.7
UniProt: Q47155
Ligands: TTP, MG
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	DNA polymerase IV (EC 2.7.7.7)	protein	342	43% helix, 23% strand	Q47155
B, C, G	DTN1	dna	17	—	—
H	DTN2C	dna	14	—	—

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · 3 copies · chains A, B, C, F, G, H
MG · Magnesium ion · metal · 4 copies · chains A, C, F, H

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	994	0.81	0.83	87	MG, TTP
2	1024	0.80	0.81	82	TTP, MG
3	666	0.74	0.81	54	empty
4	456	0.74	0.83	40	empty
5	70	0.34	0.76	15	empty

Interfaces

9 interfaces between chains.

A–B · 947 Å² buried · 24 hydrogen bonds · protein-nucleic
F–G · 899 Å² buried · 15 hydrogen bonds · protein-nucleic
B–C · 651 Å² buried · 68 hydrogen bonds · nucleic-nucleic
G–H · 638 Å² buried · 61 hydrogen bonds · nucleic-nucleic
F–H · 584 Å² buried · 22 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

5YUW · DNA polymerase IV - DNA ternary complex 6 · the same entry in another collection · chain H against H, TM-score 1.00
Q47155 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q47155) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q47155
Elsewhere: RCSB PDB 5YUW · PDBe 5YUW · UniProt Q47155

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