2DQU

Crystal form II: high resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.207

Literature

Macromolecules
Sequence Display for 2DQU

Classification: IMMUNE SYSTEM

Total Structure Weight: 48979.38

Macromolecule Entities
Molecule Chains Length Organism Details
IMMUNOGLOBULIN 6D9 L 219 Mus musculus Fragment: FAB FRAGMENT
Gene Name(s): Igkc Igk-C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
IMMUNOGLOBULIN 6D9 H 224 Mus musculus Fragment: FAB FRAGMENT
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CPD
Query on CPD

H [1-(3-DIMETHYLAMINO-PROPYL)-3-ETHYL-UREIDO]- [4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]PHOSPHINIC ACID- 2-(2,2-DIHYDRO-ACETYLAMINO)-3-HYDROXY-1-(4- NITROPHENYL)-PROPYL ESTER
C28 H36 Cl2 F3 N6 O8 P
SITLNJAUKLVJOA-CTQJRONWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CPD N/A in BindingDB
Ki: 50 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.207
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 58.70 α = 90.00
b = 63.04 β = 98.75
c = 56.56 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-05-30
  • Released Date: 2006-06-20
  • Deposition author(s): Kristensen, O., Vassylyev, D.G., Tanaka, F., Ito, N., Morikawa, K., Fujii, I.
  • Previous versions: 1HYY

Revision History

  • 2008-04-30
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance