1KQ0 | pdb_00001kq0

Human methionine aminopeptidase type II in complex with D-methionine

• PDB DOI: https://doi.org/10.2210/pdb1KQ0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2002-01-03 Released: 2003-12-09 
• Deposition Author(s): Nonato, M.C., Widom, J., Clardy, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Human methionine aminopeptidase type 2 in complex with L- and D-methionine

Nonato, M.C., Widom, J., Clardy, J.

(2006) Bioorg Med Chem Lett 16: 2580-2583

• PubMed: 16540317 
• DOI: https://doi.org/10.1016/j.bmcl.2006.02.047
• Primary Citation Related Structures: 
  1KQ0, 1KQ9


• PubMed Abstract: 
  

  Human methionine aminopeptidase type 2 (hMetAP-2) was identified as the molecular target of anti-angiogenic agents such as fumagillin and its analogues. We describe here the crystal structure of hMetAP-2 in complex with l-methionine and d-methionine at 1.9 and 2.0A resolution, respectively. The comparison of the structure of the two complexes establishes the basis of enantiomer discrimination and provides some considerations for the design of selective MetAP-2 inhibitors.

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853-1301, USA.

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: 53.34 kDa 
• Atom Count: 2,990 
• Modeled Residue Count: 354 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase 2	A	478	Homo sapiens	Mutation(s): 0  EC: 3.4.11.18
UniProt & NIH Common Fund Data Resources
Find proteins for P50579 (Homo sapiens) Explore P50579  Go to UniProtKB:  P50579
PHAROS:  P50579 GTEx:  ENSG00000111142

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MED	D [auth A]	D-METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-SCSAIBSYSA-N
TBU	E [auth A]	TERTIARY-BUTYL ALCOHOL C4 H10 O DKGAVHZHDRPRBM-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.727	α = 90
b = 98.938	β = 90
c = 100.628	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-12-09 
Deposition Author(s): Nonato, M.C., Widom, J., Clardy, J.

Revision History  

• Version 1.0: 2003-12-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary