6M9C

PSEUDOMONAS SERINE-CARBOXYL PROTEINASE (SEDOLISIN) COMPLEXED WITH THE INHIBITOR Pseudotyrostatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Inhibitor complexes of the Pseudomonas serine-carboxyl proteinase

Wlodawer, A.Li, M.Gustchina, A.Dauter, Z.Uchida, K.Oyama, H.Goldfarb, N.E.Dunn, B.M.Oda, K.

(2001) Biochemistry 40: 15602-15611

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of the serine-carboxyl proteinase from Pseudomonas sp. 101 (PSCP), complexed with a number of inhibitors, have been solved and refined at high- to atomic-level resolution. All of these inhibitors (tyrostatin, pseudo-tyrostatin, AcI ...

    Crystal structures of the serine-carboxyl proteinase from Pseudomonas sp. 101 (PSCP), complexed with a number of inhibitors, have been solved and refined at high- to atomic-level resolution. All of these inhibitors (tyrostatin, pseudo-tyrostatin, AcIPF, AcIAF, and chymostatin, as well as previously studied iodotyrostatin and pseudo-iodotyrostatin) make covalent bonds to the active site Ser287 through their aldehyde moieties, while their side chains occupy subsites S1-S4 of the enzyme. The mode of binding of the inhibitors is almost identical for their P1 and P2 side chains, while significant differences are observed for P3 and P4 (if present). Kinetic parameters for the binding of these nanomolar inhibitors to PSCP have been established and correlated with the observed mode of binding. The preferences of this enzyme for a larger side chain in P2 as well as Tyr or Phe in P1 are explained by the size, shape, and characteristics of the S2 and S1 regions of the protein structure, respectively. Networks of hydrogen bonds involving glutamic and aspartic acids have been analyzed for the atomic-resolution structure of the native enzyme. PSCP contains a calcium-binding site that consists of Asp328, Asp348, three amide carbonyl groups, and a water molecule, in almost perfect octahedral coordination. The presence of Ca(2+) cation is necessary for the activity of the enzyme.


    Organizational Affiliation

    Protein Structure Section, Macromolecular Crystallography Laboratory, and Intramural Research Support Program, SAIC Frederick, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA. wlodawer@ncifcrf.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SEDOLISIN
A
368Pseudomonas sp. (strain 101)Mutation(s): 0 
Gene Names: pcp
EC: 3.4.21.100
Find proteins for P42790 (Pseudomonas sp. (strain 101))
Go to UniProtKB:  P42790
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pseudotyrostatin
B
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002327
Query on PRD_002327
BPSEUDOTYROSTATIN (Bound Form)Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.163 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 98.270α = 90.00
b = 98.270β = 90.00
c = 83.300γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHELXLrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan13460043
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK18865 & AI28571
National Institutes of Health/National Cancer InstituteUnited Statesintramural funds

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release