1TKJ

Streptomyces griseus aminopeptidase complexed with D-Methionine

• PDB DOI: https://doi.org/10.2210/pdb1TKJ/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces griseus
• Mutation(s): No 


• Deposited: 2004-06-08 Released: 2005-06-14 
• Deposition Author(s): Reiland, V., Gilboa, R., Spungin-Bialik, A., Schomburg, D., Shoham, Y., Blumberg, S., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.151 
• R-Value Work: 0.117 

Literature

Interactions of D Amino Acids with Streptomyces griseus Aminopeptidase

Reiland, V., Gilboa, R., Spungin-Bialik, A., Schomburg, D., Shoham, Y., Blumberg, S., Shoham, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.07 kDa 
• Atom Count: 2,672 
• Modelled Residue Count: 277 
• Deposited Residue Count: 284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase	A	284	Streptomyces griseus	Mutation(s): 0  EC: 3.4.11 (PDB Primary Data), 3.4.11.24 (UniProt)
UniProt
Find proteins for P80561 (Streptomyces griseus subsp. griseus (strain JCM 4626 / CBS 651.72 / NBRC 13350 / KCC S-0626 / ISP 5235)) Explore P80561  Go to UniProtKB:  P80561

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MED	E [auth A]	D-METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-SCSAIBSYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.151 
• R-Value Work: 0.117 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.962	α = 90
b = 60.962	β = 90
c = 144.705	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-14 
Deposition Author(s): Reiland, V., Gilboa, R., Spungin-Bialik, A., Schomburg, D., Shoham, Y., Blumberg, S., Shoham, G.

Revision History  

• Version 1.0: 2005-06-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary