› 7dmf

X-ray diffraction
2.2Å resolution

A de novo protein that rigidly extends the structure of tVHS-like domain in tepsin with a new designed domain

Released:
DOI: 10.2210/pdb7dmf/pdb
Model geometry
Fit model/data
PDB entry 7dmf coloured by chain, front view.
PDB entry 7dmf coloured by chain, side view.
PDB entry 7dmf coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
A backbone-centred energy function of neural networks for protein design.
Huang B, Xu Y, Hu X, Liu Y, Liao S, Zhang J, Huang C, Hong J, Chen Q, Liu H
Nature 602 523-528 (2022)
PMID: 35140398

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-168161 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Designed protein EXTD-3 Chain: A
Molecule details ›
Chain: A
Length: 189 amino acids
Theoretical weight: 21.19 KDa
Source organism: synthetic construct
Expression system: Escherichia coli K-12

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P65
Unit cell:
a: 69.727Å b: 69.727Å c: 79.291Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.236 0.232 0.269
Expression system: Escherichia coli K-12

Quick links

Citations

6 review citations

From sequence to function through structure: Deep learning for protein design.
Ferruz et al. (2023)
5 more

2 mentions without citation

Investigation on the catalytic behavior of a novel thulium-organic framework with a planar tetranuclear {Tm4} cluster as the active center for chemical CO2 fixation.
Chen et al. (2022)
1 more

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO