3NZH | pdb_00003nzh

Crystal structure of anti-emmprin antibody 5F6 FAB

• PDB DOI: https://doi.org/10.2210/pdb3NZH/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2010-07-16 Released: 2011-07-27 
• Deposition Author(s): Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of anti-emmprin antibody 5F6 FAB

Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 48.22 kDa 
• Atom Count: 3,565 
• Modeled Residue Count: 436 
• Deposited Residue Count: 440 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5F6 LIGHT CHAIN	A [auth L]	214	Homo sapiens, Mus musculus This entity is chimeric	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5F6 HEAVY CHAIN	B [auth H]	226	Homo sapiens, Mus musculus This entity is chimeric	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO	D [auth H]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.53	α = 90
b = 129.74	β = 109.52
c = 42.39	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.L.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary