MolNFT v1 · #141167 · protein + DNA

DNA polymerase IV - ternary complex 15

5YYD: “DNA polymerase IV - ternary complex 15”. X-ray diffraction, 2 ligands (TTW, NA), 6 pockets (best druggability 0.80). MolNFT v1 #141167 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YYD
Type: protein + DNA
Length: 747 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; DTN2
EC: 2.7.7.7
UniProt: Q47155
Ligands: TTW, NA
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 42% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F, A	DNA polymerase IV (EC 2.7.7.7)	protein	342	42% helix, 23% strand	Q47155
G, B	DTN2	dna	17	—	—
H	DTN2	dna	13	—	—
C	DTN2	dna	16	—	—

Ligands and binding sites

TTW · 5'-O-[hydroxy{[hydroxy(phosphonoamino) phosphoryl]oxy}phosphoryl]thymidine · ligand · 2 copies · chains F, G, H, A, B, C
NA · Sodium ion · metal · 2 copies · chains F, A

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	933	0.80	0.83	80	TTW, NA
2	1184	0.80	0.82	85	TTW, NA
3	708	0.77	0.82	57	empty
4	729	0.73	0.79	51	empty
5	67	0.35	0.76	15	empty

Interfaces

9 interfaces between chains.

A–B · 904 Å² buried · 21 hydrogen bonds · protein-nucleic
F–G · 887 Å² buried · 19 hydrogen bonds · protein-nucleic
B–C · 649 Å² buried · 65 hydrogen bonds · nucleic-nucleic
G–H · 614 Å² buried · 52 hydrogen bonds · nucleic-nucleic
F–H · 581 Å² buried · 22 hydrogen bonds · protein-nucleic

Compared structures

5YYD · DNA polymerase IV - ternary complex 15 · 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 5YYD · PDBe 5YYD · UniProt Q47155

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