4E7N | pdb_00004e7n

Crystal Structure of AhV_TL-I, a Glycosylated Snake-venom Thrombin-like Enzyme from Agkistrodon halys

• PDB DOI: https://doi.org/10.2210/pdb4E7N/pdb

• Classification: HYDROLASE
• Organism(s): Gloydius halys
• Mutation(s): No 


• Deposited: 2012-03-18 Released: 2012-04-04 
• Deposition Author(s): Zeng, F., Li, X., Teng, M., Niu, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.205 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of AhV_TL-I, a Glycosylated Snake-venom Thrombin-like Enzyme from Agkistrodon halys

Zeng, F., Li, X., Teng, M., Niu, L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 27.03 kDa 
• Atom Count: 2,045 
• Modeled Residue Count: 238 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Snake-venom Thrombin-like Enzyme	A	238	Gloydius halys	Mutation(s): 0  EC: 3.4.21
UniProt
Find proteins for I4CHP3 (Gloydius halys) Explore I4CHP3  Go to UniProtKB:  I4CHP3
Glycosylation
Glycosylation Sites: 1

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.205 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.32	α = 90
b = 68.36	β = 90
c = 81.654	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: 2012-04-04 
Deposition Author(s): Zeng, F., Li, X., Teng, M., Niu, L.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary