6D5O

Hexagonal thermolysin (295 K) in the presence of 50% DMF

  • Classification: HYDROLASE
  • Organism(s): Bacillus thermoproteolyticus

  • Deposited: 2018-04-19 Released: 2018-09-19 
  • Deposition Author(s): Juers, D.H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00005 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order.

Juers, D.H.Farley, C.A.Saxby, C.P.Cotter, R.A.Cahn, J.K.B.Holton-Burke, R.C.Harrison, K.Wu, Z.

(2018) Acta Crystallogr D Struct Biol 74: 922-938


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermolysin
A
316Bacillus thermoproteolyticusMutation(s): 0 
Gene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
LYS
Query on LYS

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Download CCD File 
A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
VAL
Query on VAL

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Download CCD File 
A
VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
 Ligand Interaction
DMF
Query on DMF

Download SDF File 
Download CCD File 
A
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00005 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.153 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.931α = 90.00
b = 93.931β = 90.00
c = 131.656γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
CrysalisProdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-04-19 
  • Released Date: 2018-09-19 
  • Deposition Author(s): Juers, D.H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States2R15GM090248

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-31
    Type: Data collection, Database references