MolNFT v1 · #141057 · protein + DNA

DNA polymerase IV - DNA ternary complex 8

5YUX: “DNA polymerase IV - DNA ternary complex 8”. X-ray diffraction, 3 ligands (TTP, DPO, MG), 7 pockets (best druggability 0.81). MolNFT v1 #141057 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YUX
Type: protein + DNA
Length: 751 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, DPO, MG
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 4 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	DTN1	dna	17	—	—
H	DTN2	dna	15	—	—
C	DTN1	dna	18	—	—

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains F, G, H, A, B, C
DPO · Diphosphate · ligand · 2 copies · chains F, H, A, 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

7 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	935	0.81	0.83	77	empty
2	1083	0.77	0.80	67	empty
3	700	0.75	0.81	56	empty
4	958	0.74	0.78	80	DPO
5	181	0.51	0.78	29	DPO

Interfaces

9 interfaces between chains.

A–B · 931 Å² buried · 24 hydrogen bonds · protein-nucleic
F–G · 884 Å² buried · 17 hydrogen bonds · protein-nucleic
A–C · 761 Å² buried · 25 hydrogen bonds · protein-nucleic
F–H · 754 Å² buried · 26 hydrogen bonds · protein-nucleic
B–C · 680 Å² buried · 67 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

5YUX · DNA polymerase IV - DNA ternary complex 8 · the same entry in another collection · chain B against B, 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 5YUX · PDBe 5YUX · UniProt Q47155

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