MolNFT v1 · #141052 · protein + DNA

DNA polymerase IV - DNA ternary complex 2

5YUS: “DNA polymerase IV - DNA ternary complex 2”. X-ray diffraction, 2 ligands (TTP, MG), 6 pockets (best druggability 0.81). MolNFT v1 #141052 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5YUS
Type: protein + DNA
Length: 751 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; Dtn
EC: 2.7.7.7
UniProt: Q47155
Ligands: TTP, MG
Pockets: 6 · best druggability 0.81

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	Dtn	dna	18	—	—
H	Dtn	dna	14	—	—
C	Dtn	dna	17	—	—

Ligands and binding sites

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

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	944	0.81	0.83	90	TTP, MG
2	1008	0.79	0.81	78	TTP, MG
3	751	0.75	0.81	51	empty
4	694	0.73	0.79	50	empty
5	68	0.35	0.77	14	empty

Interfaces

9 interfaces between chains.

A–B · 980 Å² buried · 22 hydrogen bonds · protein-nucleic
F–G · 943 Å² buried · 22 hydrogen bonds · protein-nucleic
B–C · 654 Å² buried · 62 hydrogen bonds · nucleic-nucleic
G–H · 635 Å² buried · 58 hydrogen bonds · nucleic-nucleic
A–C · 577 Å² buried · 20 hydrogen bonds · protein-nucleic

Compared structures

5YUS · DNA polymerase IV - DNA ternary complex 2 · 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 5YUS · PDBe 5YUS · UniProt Q47155

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