MolNFT v1 · #141872 · protein + DNA

DNA polymerase IV - DNA ternary complex with 50MM MGCL2

5ZLV: “DNA polymerase IV - DNA ternary complex with 50MM MGCL2”. X-ray diffraction, 3 ligands (DPO, MG, PO4), 7 pockets (best druggability 0.77). MolNFT v1 #141872 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZLV
Type: protein + DNA
Length: 748 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; DTN2; DTN1
EC: 2.7.7.7
UniProt: Q47155
Ligands: DPO, MG, PO4
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 5 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	DTN2	dna	16	—	—
H	DTN1	dna	14	—	—
B	DTN2	dna	17	—	—
C	DTN1	dna	17	—	—

Ligands and binding sites

DPO · Diphosphate · ligand · chains A, C
MG · Magnesium ion · metal · 5 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

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	1122	0.77	0.79	70	empty
2	647	0.77	0.83	64	empty
3	974	0.75	0.78	77	DPO
4	1159	0.75	0.78	90	PO4, MG
5	193	0.60	0.83	17	empty

Interfaces

9 interfaces between chains.

A–B · 898 Å² buried · 21 hydrogen bonds · protein-nucleic
F–G · 895 Å² buried · 16 hydrogen bonds · protein-nucleic
F–H · 770 Å² buried · 24 hydrogen bonds · protein-nucleic
A–C · 763 Å² buried · 26 hydrogen bonds · protein-nucleic
B–C · 678 Å² buried · 69 hydrogen bonds · nucleic-nucleic

Compared structures

5ZLV · DNA polymerase IV - DNA ternary complex with 50mM MgCl2 · 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 5ZLV · PDBe 5ZLV · UniProt Q47155

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.