5XRF | pdb_00005xrf

Crystal structure of Da-36, a thrombin-like enzyme from Deinagkistrodon acutus

• PDB DOI: https://doi.org/10.2210/pdb5XRF/pdb

• Classification: HYDROLASE
• Organism(s): Deinagkistrodon acutus
• Mutation(s): No 


• Deposited: 2017-06-08 Released: 2018-06-13 
• Deposition Author(s): Lin, C.-C., Wu, W.-G., Fan, Q., Tian, J., Zhang, Z., Zheng, Y.
• Funding Organization(s): Yunnan Provincial Science and Technology Department

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Da-36, a thrombin-like enzyme from Deinagkistrodon acutus

Fan, Q., Tian, J., Zhang, Z., Lin, C.-C., Wu, W.-G., Zheng, Y.

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: 28.79 kDa 
• Atom Count: 2,219 
• Modeled Residue Count: 236 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Snake venom serine protease Da-36	A	242	Deinagkistrodon acutus	Mutation(s): 0
UniProt
Find proteins for J7LCB0 (Deinagkistrodon acutus) Explore J7LCB0  Go to UniProtKB:  J7LCB0
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G00395TQ GlyCosmos:  G00395TQ GlyGen:  G00395TQ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.481	α = 90
b = 87.481	β = 90
c = 104.674	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Lin, C.-C., Wu, W.-G., Fan, Q., Tian, J., Zhang, Z., Zheng, Y.

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Funding Organization	Location	Grant Number
Yunnan Provincial Science and Technology Department	China	2013FA060

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary