1NC4

Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Gd-DOTA

Structural Biology Knowledgebase: 1NC4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 1NC4

Classification: Immune system

Total Structure Weight: 95529.73

Macromolecule Entities
Molecule Chains Length Organism Details
MONOCLONAL ANTIBODY 2D12.5, LAMBDA LIGHT CHAIN A, C 215 Mus musculus Fragment: Fab
MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN B 221 Mus musculus Fragment: Fab
MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN D 221 Mus musculus Fragment: Fab

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DOF
Query on DOF

B, D (S)-2-(4-NITROBENZYL)-1,4,7,10-TETRAAZACYCLODODECANE- N,N',N'',N'''-TETRAACETATE
C23 H33 N5 O10
SQWOBSHRAUJBNP-IBGZPJMESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GD3
Query on GD3

B, D GADOLINIUM ION
Gd
RJOJUSXNYCILHH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, C CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
B L-PEPTIDE LINKING C5 H7 N O3 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.208
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 67.57 α = 90.00
b = 82.24 β = 90.00
c = 160.93 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-12-04
  • Released Date: 2003-12-16
  • Deposition author(s): Corneillie, T.M., Fisher, A.J., Meares, C.F.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update