1CVR

Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)

Structural Biology Knowledgebase: 1CVR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.163

Literature

Macromolecules
Sequence Display for 1CVR

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 48805.60

Macromolecule Entities
Molecule Chains Length Organism Details
GINGIPAIN R A 435 Porphyromonas gingivalis EC#: 3.4.22.37 IUBMB 3.5.1.2 IUBMB
Gene Name(s): rgpB prtRII rgp2 PG_0506
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
H37
Query on H37

A D-phenylalanyl-N-[(3S)-6-carbamimidamido- 1-chloro-2-oxohexan-3-yl]-L-phenylalaninamide
FFRCK (Synonym)
C25 H33 Cl N6 O3
PJFSUJMJVYGASC-HKBOAZHASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_001160
Query on PRD_001160
A D-PHENYLALANYL-N-[(3S)-6-CARBAMIMIDAMIDO-1-CHLORO-2-OXOHEXAN-3-YL]-L-PHENYLALANINAMIDE Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.163
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 51.93 α = 90.00
b = 79.92 β = 90.00
c = 99.82 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-08-24
  • Released Date: 2000-03-01
  • Deposition author(s): Eichinger, A., Beisel, H.-G.

Revision History

  • 2013-10-16
    Type: Binding sites and description | Details: --
  • 2013-10-16
    Type: Non-polymer description | Details: --
  • 2013-09-11
    Type: Non-polymer description | Details: --
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords