6B6P

Orthorhombic trypsin cryocooled to 100 K with 30% xylose as cryoprotectant

  • Classification: HYDROLASE
  • Organism(s): Bos taurus
  • Expression System: Bos taurus
  • Mutation(s): No 

  • Deposited: 2017-10-03 Released: 2017-11-01 
  • Deposition Author(s): Juers, D.H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.124 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cationic trypsin223Bos taurusMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00760
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XYS
Query on XYS
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G [auth A]alpha-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-LECHCGJUSA-N
XYP
Query on XYP
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F [auth A]beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
BEN
Query on BEN
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C [auth A]BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4
Query on SO4
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D [auth A],
E [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA
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B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.124 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.646α = 90
b = 58.315β = 90
c = 66.411γ = 90
Software Package:
Software NamePurpose
CrysalisProdata reduction
SCALAdata scaling
Cootmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Released Date: 2017-11-01 
    • Deposition Author(s): Juers, D.H.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R15GM090248

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Author supporting evidence
  • Version 1.2: 2018-09-19
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary