Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer -A2 

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

Macromolecule Content

• Total Structure Weight: 49385.00 
• Atom Count: 3374 
• Residue Count: 442 
• Unique protein chains: 2

4KMT

Crystal structure of human germline antibody 5-51/O12

• DOI: 10.2210/pdb4KMT/pdb

• Classification: IMMUNE SYSTEM
• Expression System: Homo sapiens


• Deposited: 2013-05-08 Released: 2014-03-26 
• Deposition Author(s): Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.220 
• R-Value Work: 0.171 

Literature

Antibody modeling assessment II. Structures and models.

Teplyakov, A., Luo, J., Obmolova, G., Malia, T.J., Sweet, R., Stanfield, R.L., Kodangattil, S., Almagro, J.C., Gilliland, G.L.

(2014) Proteins 82: 1563-1582

• PubMed: 24633955 
• DOI: 10.1002/prot.24554
• Primary Citation of Related Structures:  
  4MAU, 4M7K, 4M6O, 4M6M, 4KQ4


• PubMed Abstract: 
  

To assess the state-of-the-art in antibody structure modeling, a blinded study was conducted. Eleven unpublished Fab crystal structures were used as a benchmark to compare Fv models generated by seven structure prediction methodologies. In the first round, each participant submitted three non-ranked complete Fv models for each target. In the second round, CDR-H3 modeling was performed in the context of the correct environment provided by the crystal structures with CDR-H3 removed. In this report we describe the reference structures and present our assessment of the models. Some of the essential sources of errors in the predictions were traced to the selection of the structure template, both in terms of the CDR canonical structures and VL/VH packing. On top of this, the errors present in the Protein Data Bank structures were sometimes propagated in the current models, which emphasized the need for the curated structural database devoid of errors. Modeling non-canonical structures, including CDR-H3, remains the biggest challenge for antibody structure prediction.

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Organizational Affiliation: 

Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania, 19477.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
light chain O12/KAPPA	L	214	N/A
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
heavy chain 5-51/CNTO888/IGG1	H	228	N/A
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	H, L	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H, L	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NHE	H, L	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID N-CYCLOHEXYLTAURINE; CHES C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.220 
• R-Value Work: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 63.670	α = 90.00
b = 73.830	β = 90.00
c = 103.050	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
REFMAC	refinement
XDS	data scaling
CrystalClear	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-08 
• Released Date: 2014-03-26 
• Deposition Author(s): Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.L.

Revision History 

• Version 1.0: 2014-03-26
  Type: Initial release
• Version 1.1: 2014-04-02
  Type: Database references
• Version 1.2: 2014-08-06
  Type: Database references