1V7P

Structure of EMS16-alpha2-I domain complex

• PDB DOI: https://doi.org/10.2210/pdb1V7P/pdb

• Classification: TOXIN/CELL ADHESION
• Organism(s): Echis multisquamatus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-12-19 Released: 2004-09-07 
• Deposition Author(s): Horii, K., Okuda, D., Morita, T., Mizuno, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.188 

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.

Macromolecule Content

• Total Structure Weight: 53.3 kDa 
• Atom Count: 4,153 
• Modelled Residue Count: 454 
• Deposited Residue Count: 462 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EMS16 A chain	A	134	Echis multisquamatus	Mutation(s): 0
UniProt
Find proteins for Q7T2Q1 (Echis multisquamatus) Explore Q7T2Q1  Go to UniProtKB:  Q7T2Q1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EMS16 B chain	B	128	Echis multisquamatus	Mutation(s): 1
UniProt
Find proteins for Q7T2Q0 (Echis multisquamatus) Explore Q7T2Q0  Go to UniProtKB:  Q7T2Q0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-2	C	200	Homo sapiens	Mutation(s): 3
UniProt & NIH Common Fund Data Resources
Find proteins for P17301 (Homo sapiens) Explore P17301  Go to UniProtKB:  P17301
PHAROS:  P17301 GTEx:  ENSG00000164171

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN	G [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.188 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.766	α = 90
b = 38.449	β = 91.52
c = 69.524	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-07 
Deposition Author(s): Horii, K., Okuda, D., Morita, T., Mizuno, H.

Revision History  

• Version 1.0: 2004-09-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2021-11-10
  Changes: Database references, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection