1KKK | pdb_00001kkk

Thermolysin complexed with Z-L-Aspartic Acid (benzyloxycarbonyl-L-Aspartic Acid)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.189 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure analyses of thermolysin in complex with its inhibitors.

Senda, M., Senda, T., Kidokoro, S.

To be published.

Macromolecule Content 

  • Total Structure Weight: 34.89 kDa 
  • Atom Count: 2,691 
  • Modeled Residue Count: 316 
  • Deposited Residue Count: 316 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thermolysin316Bacillus thermoproteolyticusMutation(s): 0 
EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus)
Explore P00800 
Go to UniProtKB:  P00800
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00800
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PHQ

Query on PHQ


Download:Ideal Coordinates CCD File
G [auth A]benzyl chlorocarbonate
C8 H7 Cl O2
HSDAJNMJOMSNEV-UHFFFAOYSA-N
ASP

Query on ASP


Download:Ideal Coordinates CCD File
H [auth A]ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.189 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.676α = 90
b = 93.676β = 90
c = 131.515γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations