7KD2

Ricin bound to VHH antibody V11B2

• PDB DOI: https://doi.org/10.2210/pdb7KD2/pdb

• Classification: TOXIN
• Organism(s): Ricinus communis, Vicugna pacos
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-10-07 Released: 2021-08-04 
• Deposition Author(s): Rudolph, M.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.280 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 74.68 kDa 
• Atom Count: 5,262 
• Modelled Residue Count: 634 
• Deposited Residue Count: 655 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin chain A	A	267	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin chain B	B	262	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH antibody V11B2	C	126	Vicugna pacos	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80587NA GlyCosmos:  G80587NA GlyGen:  G80587NA

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth A], L [auth B], Q [auth C], R [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], P [auth B], S [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.280 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.607	α = 90
b = 99.559	β = 90
c = 111.283	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Rudolph, M.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201400021C

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description