MolNFT v1 · #141058 · protein + DNA

DNA polymerase IV - DNA ternary complex 9

5YUY: “DNA polymerase IV - DNA ternary complex 9”. X-ray diffraction, 3 ligands (DPO, TTP, MG), 9 pockets (best druggability 0.80). MolNFT v1 #141058 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YUY
Type: protein + DNA
Length: 755 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; DTN1; Dtn
EC: 2.7.7.7
UniProt: Q47155
Ligands: DPO, TTP, MG
Pockets: 9 · best druggability 0.80

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	18	—	—
H	Dtn	dna	17	—	—
C	Dtn	dna	18	—	—

Ligands and binding sites

DPO · Diphosphate · ligand · 2 copies · chains F, H, A, C
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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	835	0.80	0.83	63	empty
2	1150	0.78	0.80	70	empty
3	396	0.74	0.85	36	empty
4	671	0.72	0.79	49	empty
5	221	0.58	0.80	30	DPO

Interfaces

9 interfaces between chains.

A–B · 1023 Å² buried · 25 hydrogen bonds · protein-nucleic
F–G · 952 Å² buried · 20 hydrogen bonds · protein-nucleic
A–C · 767 Å² buried · 25 hydrogen bonds · protein-nucleic
F–H · 740 Å² buried · 28 hydrogen bonds · protein-nucleic
B–C · 683 Å² buried · 66 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

5YUY · DNA polymerase IV - DNA ternary complex 9 · 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 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 5YUY · PDBe 5YUY · UniProt Q47155

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