› 4nvh

X-ray diffraction
1.24Å resolution

Predicting protein conformational response in prospective ligand discovery

Released:
DOI: 10.2210/pdb4nvh/pdb
PDB entry 4nvh coloured by chain, front view.
PDB entry 4nvh coloured by chain, side view.
PDB entry 4nvh coloured by chain, top view.
Source organism: Saccharomyces cerevisiae RM11-1a
Primary publication:
Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.
Fischer M, Coleman RG, Fraser JS, Shoichet BK
Nat Chem 6 575-83 (2014)
PMID: 24950326

Function and Biology Details

Reaction catalysed: 
2 ferrocytochrome c + H(2)O(2) = 2 ferricytochrome c + 2 H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109881 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peroxidase Chain: B
Molecule details ›
Chain: B
Length: 289 amino acids
Theoretical weight: 32.93 KDa
Source organism: Saccharomyces cerevisiae RM11-1a
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B3LRE1 (Residues: 72-362; Coverage: 80%)
Gene name: SCRG_04081
Sequence domains: Peroxidase
Structure domains:

Ligands and Environments


Cofactor: Ligand HEM 1 x HEM
1 bound ligand:
Ligand 2NB 1 x 2NB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P212121
Unit cell:
a: 50.92Å b: 74.72Å c: 106.71Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.129 0.128 0.145
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

14 review citations

Docking Screens for Novel Ligands Conferring New Biology.
Irwin et al. (2016)
13 more

2 mentions without citation

π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures.
Bauzá et al. (2019)
1 more