4FYR

Human aminopeptidase N (CD13) in complex with bestatin

Structural Biology Knowledgebase: 4FYR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.167

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4FYR

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 107205.41

Macromolecule Entities
Molecule Chains Length Organism Details
Aminopeptidase N A 903 Homo sapiens EC#: 3.4.11.2 IUBMB
Gene Name(s): ANPEP Gene View APN CD13 PEPN

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BES
Query on BES

A 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)- 4-METHYL-PENTANOIC ACID
BESTATIN (Synonym)
C16 H24 N2 O4
VGGGPCQERPFHOB-RDBSUJKOSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

A ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BES IC50: 2400 - >471600 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.167
  • Space Group: P 64
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 158.07 α = 90.00
b = 158.07 β = 90.00
c = 114.81 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-07-05
  • Released Date: 2012-09-05
  • Deposition author(s): Wong, A.H., Rini, J.M.

Revision History

  • 2012-11-14
    Type: Citation | Details: Citation update