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DNA polymerase IV - ternary complex 16

Analyse DNA polymerase IV - ternary complex 16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YYE
Type: protein + DNA
Length: 750 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, MG
Pockets: 7 · 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, C	DTN2	dna	17	—	—
H	DTN2	dna	14	—	—
B	DTN2	dna	18	—	—

Ligands and binding sites

TTW · 5'-O-[hydroxy{[hydroxy(phosphonoamino) phosphoryl]oxy}phosphoryl]thymidine · 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

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	1058	0.80	0.81	83	TTW, MG
2	746	0.79	0.83	69	TTW, MG
3	848	0.74	0.79	60	empty
4	724	0.72	0.79	52	empty
5	180	0.58	0.82	16	empty

Interfaces

9 interfaces between chains.

A–B · 963 Å² buried · 25 hydrogen bonds · protein-nucleic
F–G · 890 Å² buried · 19 hydrogen bonds · protein-nucleic
G–H · 640 Å² buried · 63 hydrogen bonds · nucleic-nucleic
B–C · 638 Å² buried · 67 hydrogen bonds · nucleic-nucleic
A–C · 580 Å² buried · 21 hydrogen bonds · protein-nucleic

Compared structures

5YYE · DNA polymerase IV - ternary complex 16 · 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 5YYE · PDBe 5YYE · UniProt Q47155

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