MolNFT v1 · #141063 · protein + DNA

DNA polymerase IV - DNA ternary complex 7

5YV3: “DNA polymerase IV - DNA ternary complex 7”. X-ray diffraction, 3 ligands (TTP, DPO, MG), 7 pockets (best druggability 0.80). MolNFT v1 #141063 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YV3
Type: protein + DNA
Length: 750 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 0.80

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F, A	DNA polymerase IV (EC 2.7.7.7)	protein	342	43% helix, 23% strand	Q47155
G, B, C	DTN1	dna	17	—	—
H	DTN2	dna	15	—	—

Ligands and binding sites

TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains F, G, H, A, B, C
DPO · Diphosphate · ligand · chains F, H
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	903	0.80	0.83	72	empty
2	1033	0.80	0.81	82	MG, TTP
3	896	0.75	0.79	60	empty
4	727	0.73	0.79	51	empty
5	236	0.53	0.77	32	DPO

Interfaces

9 interfaces between chains.

A–B · 946 Å² buried · 25 hydrogen bonds · protein-nucleic
F–G · 890 Å² buried · 17 hydrogen bonds · protein-nucleic
F–H · 758 Å² buried · 22 hydrogen bonds · protein-nucleic
G–H · 668 Å² buried · 62 hydrogen bonds · nucleic-nucleic
B–C · 649 Å² buried · 68 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 3 covalent (covalent ligand).

Compared structures

5YV3 · DNA polymerase IV - DNA ternary complex 7 · 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 5YV3 · PDBe 5YV3 · UniProt Q47155

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