MolNFT v2 · #225402 · protein + DNA

Cryo-EM structure of ATP-DNA-MuB filaments

8XVB · DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*…: “Cryo-EM structure of ATP-DNA-MuB filaments”. Electron microscopy at 3.4, 1 ligand (ATP), 20 pockets (best druggability 0.78). MolNFT v2 #225402 on GenesisL1: 3D…

PDB: 8XVB
Type: protein + DNA
Length: 2,016 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.4
Source: Escherichia phage Mu; SYNTHETIC CONSTRUCT
Molecule: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')…
EC: 3.6.1.-
UniProt: P03763
Ligands: ATP
Pockets: 20 · best druggability 0.78

Structure

electron microscopy · resolution 3.4 · 3 distinct chains · 56% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I	DNA (5'-D(PAPAPAPAPAPAPAPAPAPAPAPAPAPAPAPAPAPAPAPAPAPAPAPA)-3')	dna	24	—	—
A, B, C, D, E, F, G, H	ATP-dependent target DNA activator B (EC 3.6.1.-)	protein	246	56% helix, 10% strand	P03763
J	DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3')	dna	24	—	—

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, F, B, C, D, E, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	692	0.78	0.83	85	ATP
2	676	0.78	0.83	70	ATP
3	719	0.77	0.82	72	ATP
4	597	0.77	0.83	57	ATP
5	675	0.77	0.82	67	ATP

Interfaces

32 interfaces between chains.

B–C · 1708 Å² buried · 28 hydrogen bonds · protein-protein
A–F · 1708 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1707 Å² buried · 32 hydrogen bonds · protein-protein
F–G · 1693 Å² buried · 32 hydrogen bonds · protein-protein
G–H · 1692 Å² buried · 34 hydrogen bonds · protein-protein

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 P03763
Elsewhere: RCSB PDB 8XVB · PDBe 8XVB · UniProt P03763

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