Research workbench

DNA polymerase IV - DNA ternary complex 1

Analyse DNA polymerase IV - DNA ternary complex 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YUR
Type: protein + DNA
Length: 744 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; Dtn
EC: 2.7.7.7
UniProt: Q47155
Ligands: TTP, NA
Pockets: 8 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 42% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F, A	DNA polymerase IV (EC 2.7.7.7)	protein	342	42% helix, 23% strand	Q47155
G	Dtn	dna	15	—	—
H	Dtn	dna	12	—	—
B	Dtn	dna	16	—	—
C	Dtn	dna	17	—	—

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains F, G, H, A, B, C
NA · Sodium ion · metal · 2 copies · chains F, A

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1082	0.80	0.82	77	TTP, NA
2	743	0.78	0.83	53	empty
3	717	0.76	0.81	54	empty
4	661	0.72	0.79	49	empty
5	235	0.63	0.82	26	TTP, NA

Interfaces

9 interfaces between chains.

A–B · 869 Å² buried · 21 hydrogen bonds · protein-nucleic
F–G · 845 Å² buried · 20 hydrogen bonds · protein-nucleic
B–C · 648 Å² buried · 68 hydrogen bonds · nucleic-nucleic
F–H · 600 Å² buried · 21 hydrogen bonds · protein-nucleic
A–C · 574 Å² buried · 20 hydrogen bonds · protein-nucleic

Compared structures

5YUR · DNA polymerase IV - DNA ternary complex 1 · the same entry in another collection · chain C against C, TM-score 1.00
Q47155 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q47155) · a predicted model of the same protein · chain F 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 5YUR · PDBe 5YUR · UniProt Q47155

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