8ZM5

Crystal structure of Thermolysin (Dose II)

  • Classification: HYDROLASE
  • Organism(s): Bacillus thermoproteolyticus
  • Mutation(s): No 

  • Deposited: 2024-05-22 Released: 2024-06-05 
  • Deposition Author(s): Nam, K.H.
  • Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of Thermolysin (Dose II)

Nam, K.H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LYS
Query on LYS

Download Ideal Coordinates CCD File 
C [auth A]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
ILE
Query on ILE

Download Ideal Coordinates CCD File 
B [auth A]ISOLEUCINE
C6 H13 N O2
AGPKZVBTJJNPAG-WHFBIAKZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.081α = 90
b = 93.081β = 90
c = 128.694γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-06-05 
  • Deposition Author(s): Nam, K.H.

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2021R1I1A1A01050838

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release