5TMN

Slow-and fast-binding inhibitors of thermolysin display different modes of binding. crystallographic analysis of extended phosphonamidate transition-state analogues

Structural Biology Knowledgebase: 5TMN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Observed: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 5TMN

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 35059.79

Macromolecule Entities
Molecule Chains Length Organism Details
THERMOLYSIN E 316 Bacillus thermoproteolyticus EC#: 3.4.24.27 IUBMB
Gene Name(s): npr

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0PJ
Query on 0PJ

N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]- L-leucyl-L-leucine
ZGPLL (Synonym)
C21 H34 N3 O7 P
ASUDVBNLLSQCDJ-ROUUACIJSA-N
Ligand Explorer
 
JSmol
CA
Query on CA

CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
ZN
Query on ZN

ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0PJ N/A in BindingDB
Ki: 9.1 nM  BindingMOAD
N/A in PDBbind
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000654 E CBZ-GLY-P-LEU-LEU (ZGPLL) Peptide-like /
Enzyme Inhibitor
Ligand Explorer

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Observed: 0.177
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 94.10 α = 90.00
b = 94.10 β = 90.00
c = 131.40 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1987-06-29
  • Released Date: 1989-01-09
  • Deposition author(s): Holden, H.M., Tronrud, D.E., Monzingo, A.F., Weaver, L.H., Matthews, B.W.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2012-06-13
    Type: Biological assembly | Details: update remark 350
  • 2011-07-13
    Type: Flag nonstandard coordinate frame | Details: Tagged nonstandard coordinate frame
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords