1D6V

CONFORMATION EFFECTS IN BIOLOGICAL CATALYSIS INTRODUCED BY OXY-COPE ANTIBODY MATURATION

Structural Biology Knowledgebase: 1D6V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.224

Literature

Macromolecules
Sequence Display for 1D6V

Classification: IMMUNE SYSTEM

Total Structure Weight: 47955.85

Macromolecule Entities
Molecule Chains Length Organism Details
CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (LIGHT CHAIN) L 211 Homo sapiens Mus musculus Fragment: CHIMERIC FAB FRAGMENT
Mutation: N34S, T51A
Details: THE PROTEIN WAS PRODUCED AS A CHIMERIC FAB FRAGMENT. THE VARIABLE DOMAINS (CHAINS A,L 1-107, CHAINS B,H 1-113) ARE MURINE. THE CONSTANT DOMAINS (CHAINS A, L 108-211 AND CHAINS B,H 113-214) ARE HUMAN.
Gene Name(s): IGKC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CHIMERIC GERMLINE PRECURSOR OF OXY-COPE CATALYTIC ANTIBODY AZ-28 (HEAVY CHAIN) H 221 Homo sapiens Mus musculus Fragment: CHIMERIC FAB FRAGMENT
Mutation: F32Y, G56S, H58N, K73T
Details: THE PROTEIN WAS PRODUCED AS A CHIMERIC FAB FRAGMENT. THE VARIABLE DOMAINS (CHAINS A,L 1-107, CHAINS B,H 1-113) ARE MURINE. THE CONSTANT DOMAINS (CHAINS A, L 108-211 AND CHAINS B,H 113-214) ARE HUMAN.
Gene Name(s): IGHG1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

H (1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL- 1-CYCLOHEXANOL
OXY-COPE-HAPTEN (Synonym)
C23 H27 N O4
OBWILOKKNDYPLX-HBMCJLEFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

L CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
HOP N/A in BindingDB
Kd: 670 nM  BindingMOAD
Kd: 670 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.224
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 52.72 α = 90.00
b = 64.45 β = 99.09
c = 73.87 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-10-15
  • Released Date: 2000-02-09
  • Deposition author(s): Mundorff, E.C., Hanson, M.A., Schultz, P.G., Stevens, R.C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4