3VN4

Crystal structure of the exosite-containing fragment of human ADAMTS13 (P475S mutant)

• PDB DOI: https://doi.org/10.2210/pdb3VN4/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2011-12-21 Released: 2012-12-26 
• Deposition Author(s): Nakayama, D., Akiyama, M., Takeda, S., Kokame, K., Takagi, J., Miyata, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.277 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 

Literature

Structural analysis and biochemical studies of ADAMTS13 P475S mutant

Nakayama, D., Akiyama, M., Takeda, S., Kokame, K., Takagi, J., Miyata, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.49 kDa 
• Atom Count: 3,013 
• Modelled Residue Count: 375 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A disintegrin and metalloproteinase with thrombospondin motifs 13	A	410	Homo sapiens	Mutation(s): 1  Gene Names: ADAMTS13 EC: 3.4.24.87
UniProt & NIH Common Fund Data Resources
Find proteins for Q76LX8 (Homo sapiens) Explore Q76LX8  Go to UniProtKB:  Q76LX8
PHAROS:  Q76LX8 GTEx:  ENSG00000160323

Oligosaccharides

Help

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose	C	2		O-Glycosylation
Glycosylation Resources
GlyTouCan:  G36855WW GlyCosmos:  G36855WW GlyGen:  G36855WW

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA	E [auth A]	beta-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.277 
• R-Value Work: 0.229 
• R-Value Observed: 0.232 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.378	α = 90
b = 53.243	β = 111.56
c = 76.615	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): Nakayama, D., Akiyama, M., Takeda, S., Kokame, K., Takagi, J., Miyata, T.

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary