3FXP | pdb_00003fxp

Thermolysin inhibition

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.265 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.175 (DCC) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

Thermolysin in complex with triazolic inhibitor

Englert, L., Sun, D., Koert, U., Heine, A., Klebe, G.

To be published.

Macromolecule Content 

  • Total Structure Weight: 35.21 kDa 
  • Atom Count: 2,615 
  • 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
D38

Query on D38


Download:Ideal Coordinates CCD File
G [auth A]N~2~-[(2S)-2-{[1-(4-carboxybenzyl)-1H-1,2,3-triazol-4-yl]methyl}-3-methylbutanoyl]-L-lysine
C22 H31 N5 O5
ZFYKXBBWZOQIRM-OALUTQOASA-N
GLO

Query on GLO


Download:Ideal Coordinates CCD File
H [auth A]D-glucose
C6 H12 O6
GZCGUPFRVQAUEE-SLPGGIOYSA-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: 2.05 Å
  • R-Value Free:  0.265 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.175 (DCC) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.893α = 90
b = 92.893β = 90
c = 128.537γ = 120
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing

Structure Validation

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Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Structure summary