Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53493.29 
• Atom Count: 2815 
• Residue Count: 478 
• Unique protein chains: 1

1B6A

HUMAN METHIONINE AMINOPEPTIDASE 2 COMPLEXED WITH TNP-470

• DOI: 10.2210/pdb1B6A/pdb

• Classification: ANGIOGENESIS INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda multiple nucleopolyhedrovirus


• Deposited: 1999-01-13 Released: 2000-01-13 
• Deposition Author(s): Liu, S., Clardy, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.216 
• R-Value Work: 0.187 

Literature

Structure of human methionine aminopeptidase-2 complexed with fumagillin.

Liu, S., Widom, J., Kemp, C.W., Crews, C.M., Clardy, J.

(1998) Science 282: 1324-1327

• PubMed: 9812898 
• Primary Citation of Related Structures:  
  1BOA, 1BN5, 1B59


• PubMed Abstract: 
  

The fungal metabolite fumagillin suppresses the formation of new blood vessels, and a fumagillin analog is currently in clinical trials as an anticancer agent. The molecular target of fumagillin is methionine aminopeptidase-2 (MetAP-2). A 1.8 A resolution crystal structure of free and inhibited human MetAP-2 shows a covalent bond formed between a reactive epoxide of fumagillin and histidine-231 in the active site of MetAP-2. Extensive hydrophobic and water-mediated polar interactions with other parts of fumagillin provide additional affinity. Fumagillin-based drugs inhibit MetAP-2 but not MetAP-1, and the three-dimensional structure also indicates the likely determinants of this specificity. The structural basis for fumagillin's potency and specificity forms the starting point for structure-based drug design.

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Organizational Affiliation: 

J. Clardy, Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853-1301, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
METHIONINE AMINOPEPTIDASE	A	478	Homo sapiens	Mutation(s): 0  Gene Names: METAP2 (MNPEP, P67EIF2) EC: 3.4.11.18
Find proteins for P50579 (Homo sapiens) Go to Gene View: METAP2 Go to UniProtKB:  P50579

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
TN4	A	(1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate TNP-470 (Open form) C19 H30 Cl N O6 OUUSPVSSNHLIGE-AGYLCKTBSA-N
CO	A	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
TN4	IC50: 1 - 1320 nM (100) BINDINGDB
TN4	Ki: 1 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.216 
• R-Value Work: 0.187 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 89.558	α = 90.00
b = 99.060	β = 90.00
c = 101.508	γ = 90.00

Software Package:

Software Name	Purpose
SYNCHROTRON	data collection
CNS	refinement
SOFTWARE	data reduction
SCALA	data scaling
CNS	phasing
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-01-13 
• Released Date: 2000-01-13 
• Deposition Author(s): Liu, S., Clardy, J.C.

Revision History 

• Version 1.0: 2000-01-13
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2011-08-31
  Type: Non-polymer description