Research workbench

DNA polymerase IV - DNA ternary complex 4

Analyse DNA polymerase IV - DNA ternary complex 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YUU
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; DTN2
EC: 2.7.7.7
UniProt: Q47155
Ligands: TTP, MG
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F, A	DNA polymerase IV (EC 2.7.7.7)	protein	342	44% helix, 23% strand	Q47155
G, B, C	DTN1	dna	17	—	—
H	DTN2	dna	14	—	—

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains F, G, H, A, B, C
MG · Magnesium ion · metal · 4 copies · chains F, H, A, C

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	1023	0.81	0.83	87	TTP, MG
2	1034	0.79	0.81	82	TTP, MG
3	529	0.75	0.83	47	empty
4	702	0.73	0.79	53	empty
5	79	0.36	0.76	16	empty

Interfaces

9 interfaces between chains.

A–B · 931 Å² buried · 22 hydrogen bonds · protein-nucleic
F–G · 893 Å² buried · 18 hydrogen bonds · protein-nucleic
B–C · 651 Å² buried · 66 hydrogen bonds · nucleic-nucleic
G–H · 643 Å² buried · 63 hydrogen bonds · nucleic-nucleic
F–H · 592 Å² buried · 20 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5YUU · DNA polymerase IV - DNA ternary complex 4 · 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 5YUU · PDBe 5YUU · UniProt Q47155

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.