7JKM | pdb_00007jkm

REGN1 Human Fab in complex with anti-Kappa VHH domain

• PDB DOI: https://doi.org/10.2210/pdb7JKM/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Lama glama
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-28 Released: 2021-08-04 
• Deposition Author(s): Dennis, T.N., de la Cruz, M., Williams, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Verification of a Fab binding nanobody for crystallization studies

de la Cruz, M., King, J., Truong, T., Dennis, T.N., Williams, J.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 60.73 kDa 
• Atom Count: 4,869 
• Modeled Residue Count: 553 
• Deposited Residue Count: 561 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REGN1 Antibody Light Chain	A [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REGN1 Antibody Heavy Chain	B [auth H]	225	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-Kappa VHH domain nanobody	C [auth K]	121	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.365	α = 90
b = 75.93	β = 90.814
c = 64.003	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Dennis, T.N., de la Cruz, M., Williams, J.C.

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary