3N56 | pdb_00003n56

Crystal Structure of human Insulin-degrading enzyme (IDE) in complex with human B-type natriuretic peptide (BNP)

• PDB DOI: https://doi.org/10.2210/pdb3N56/pdb

• Classification: HYDROLASE/HORMONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-05-24 Released: 2010-11-17 
• Deposition Author(s): Funke, T., Guo, Q., Tang, W.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.243 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of human Insulin-degrading enzyme (IDE) in complex with human B-type natriuretic peptide (BNP)

Ralat, L.A., Funke, T., Ren, M., Guo, Q., Dickey, D.M., Potter, L.R., Tang, W.-J.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 236.38 kDa 
• Atom Count: 15,654 
• Modeled Residue Count: 1,906 
• Deposited Residue Count: 2,044 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-degrading enzyme	A, B	990	Homo sapiens	Mutation(s): 14  Gene Names: HCG_1810909, IDE, RP11-366I13.1-001 EC: 3.4.24.56
UniProt & NIH Common Fund Data Resources
Find proteins for P14735 (Homo sapiens) Explore P14735  Go to UniProtKB:  P14735
PHAROS:  P14735 GTEx:  ENSG00000119912

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Natriuretic peptides B	C, D	32	Homo sapiens	Mutation(s): 0  Gene Names: NPPB
UniProt & NIH Common Fund Data Resources
Find proteins for P16860 (Homo sapiens) Explore P16860  Go to UniProtKB:  P16860
PHAROS:  P16860 GTEx:  ENSG00000120937

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIO	F [auth A], G [auth B]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N
ZN	E [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.243 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 264.036	α = 90
b = 264.036	β = 90
c = 90.645	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Funke, T., Guo, Q., Tang, W.-J.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description