6KKF | pdb_00006kkf

Crystal structure of proteinase K complexed with a triglycine

  • Classification: HYDROLASE
  • Organism(s): Parengyodontium album
  • Mutation(s): No 

  • Deposited: 2019-07-25 Released: 2019-09-25 
  • Deposition Author(s): Nam, K.H.
  • Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.218 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Triglycine-Based Approach for Identifying the Substrate Recognition Site of an Enzyme

Nam, K.H.

(2019) Crystals (Basel) 9

Macromolecule Content 

  • Total Structure Weight: 29.2 kDa 
  • Atom Count: 2,334 
  • Modeled Residue Count: 278 
  • Deposited Residue Count: 279 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteinase K279Parengyodontium albumMutation(s): 0 
EC: 3.4.21.64
UniProt
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06873
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.512α = 90
b = 67.685β = 111.393
c = 43.592γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2019-09-25 
    • Deposition Author(s): Nam, K.H.
Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2017R1D1A1B03033087
National Research Foundation (Korea)Korea, Republic Of2017M3A9F6029736

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary