1NC4

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

• PDB DOI: https://doi.org/10.2210/pdb1NC4/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


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

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Experimental Data Snapshot

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 95.53 kDa 
• Atom Count: 6,944 
• Modelled Residue Count: 860 
• Deposited Residue Count: 872 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MONOCLONAL ANTIBODY 2D12.5, LAMBDA LIGHT CHAIN	A, C	215	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN	B	221	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN	D	221	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DOF	F [auth B], J [auth D]	(S)-2-(4-NITROBENZYL)-1,4,7,10-TETRAAZACYCLODODECANE-N,N',N'',N'''-TETRAACETATE C23 H33 N5 O10 SQWOBSHRAUJBNP-IBGZPJMESA-N
NAG	I [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GD3	G [auth B], K [auth D]	GADOLINIUM ION Gd RJOJUSXNYCILHH-UHFFFAOYSA-N
CL	E [auth A], H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	B	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.569	α = 90
b = 82.239	β = 90
c = 160.934	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2003-12-16
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2019-12-25
  Changes: Derived calculations, Polymer sequence
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 2.2: 2023-08-16
  Changes: Data collection, Database references, Refinement description, Structure summary