MolNFT v1 · #141060 · protein + DNA

DNA polymerase IV - DNA ternary complex 12

5YV0: “DNA polymerase IV - DNA ternary complex 12”. X-ray diffraction, 4 ligands (DPO, TTP, MG), 6 pockets (best druggability 0.81). MolNFT v1 #141060 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YV0
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: DPO, TTP, MG, PO4
Pockets: 6 · best druggability 0.81

Structure

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

Ligands and binding sites

DPO · Diphosphate · ligand · chains A, C
TTP · Thymidine-5'-triphosphate · ligand · chains A, B, C
MG · Magnesium ion · metal · 4 copies · chains F, H, A, C
PO4 · Phosphate ion · ion · 2 copies · chains F, H

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	1025	0.81	0.83	76	empty
2	1143	0.78	0.80	72	empty
3	1169	0.76	0.78	89	PO4
4	990	0.75	0.78	78	DPO
5	72	0.36	0.77	17	empty

Interfaces

9 interfaces between chains.

A–B · 925 Å² buried · 23 hydrogen bonds · protein-nucleic
F–G · 897 Å² buried · 18 hydrogen bonds · protein-nucleic
F–H · 758 Å² buried · 28 hydrogen bonds · protein-nucleic
A–C · 753 Å² buried · 25 hydrogen bonds · protein-nucleic
B–C · 681 Å² buried · 66 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

5YV0 · DNA polymerase IV - DNA ternary complex 12 · the same entry in another collection · chain A against A, 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 5YV0 · PDBe 5YV0 · UniProt Q47155

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