6QKD | pdb_00006qkd

CRYSTAL STRUCTURE OF vhh-based FAB-fragment of antibody BCD-085

• PDB DOI: https://doi.org/10.2210/pdb6QKD/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Lama glama
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2019-01-29 Released: 2019-07-24 
• Deposition Author(s): Kostareva, O.S., Kolyadenko, I.A., Ulitin, A.B., Ekimova, V.M., Evdokimov, S.R., Garber, M.B., Tishchenko, T.V., Gabdulkhakov, A.G.
• Funding Organization(s): Russian Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Models: experimental

Literature

Fab Fragment of VHH-Based Antibody Netakimab: Crystal Structure and Modeling Interaction with Cytokine IL-17A

Kostareva, O.S., Kolyadenko, I.A., Ulitin, A.B., Ekimova, V.M., Evdokimov, S.R., Garber, M.B., Tishchenko, T.V., Gabdulkhakov, A.G.

(2019) Crystals (Basel) 

• DOI: https://doi.org/10.3390/cryst9030177

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 Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 190.79 kDa 
• Atom Count: 13,541 
• Modeled Residue Count: 1,742 
• Deposited Residue Count: 1,772 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB HEAVY CHAIN	A [auth H], B [auth I], C [auth J], D [auth K]	228	Lama glama	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB LIGHT CHAIN	E [auth L], F [auth M], G [auth O], H [auth T]	215	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth H], J [auth I], L [auth K], M [auth K], O [auth L], P [auth L], Q [auth M], R [auth M], S [auth O], T	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	K [auth I], N [auth K], U [auth T]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.228 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.56	α = 90
b = 111.92	β = 90
c = 165.43	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Kostareva, O.S., Kolyadenko, I.A., Ulitin, A.B., Ekimova, V.M., Evdokimov, S.R., Garber, M.B., Tishchenko, T.V., Gabdulkhakov, A.G.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	17-74-10156

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary