3T8F

Thermolysin In Complex With UBTLN34

Structural Biology Knowledgebase: 3T8F SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.159
  • R-Value Work: 0.142

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3T8F

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35730.76

Macromolecule Entities
Molecule Chains Length Organism Details
Thermolysin A 316 Bacillus thermoproteolyticus EC#: 3.4.24.27 IUBMB
Fragment: mature form (UNP residues 233-548)
Gene Name(s): npr

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UBU
Query on UBU

A N-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]- N-ethyl-L-leucinamide
C17 H28 N3 O5 P
AYDYEZVQGYFZKJ-HNNXBMFYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
UBU Ki: 289 - 291 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000985 (PHQ,PGL,LNE) A N-[(R)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-ETHYL-L-LEUCINAMIDE Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.159
  • R-Value Work: 0.142
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 92.40 α = 90.00
b = 92.40 β = 90.00
c = 131.20 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-08-01
  • Released Date: 2012-08-01
  • Deposition author(s): Biela, A., Heine, A., Klebe, G.

Revision History

  • 2014-02-12
    Type: Citation | Details: Citation update
  • 2012-12-12
    Type: Other | Details: Add PRD info