4M1C | pdb_00004m1c

Crystal Structure Analysis of Fab-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Amyloid-Beta (1-40)

PDB DOI: https://doi.org/10.2210/pdb4M1C/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-08-02 Released: 2014-08-06
Deposition Author(s): McCord, L.M., Liang, W., Farcasanu, M., Scherpelz, K., Meredith, S.C., Koide, S., Tang, W.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.270 (Depositor), 0.270 (DCC)
R-Value Work:
0.228 (Depositor), 0.233 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure Analysis of Fab-Bound Human Insulin Degrading Enzyme (IDE) in Complex with Amyloid-Beta (1-40)

McCord, L.A., Liang, W., Farcasanu, M., Scherpelz, K., Meredith, S.C., Koide, S., Tang, W.J.

To be published.

Macromolecule Content

Total Structure Weight: 346.29 kDa
Atom Count: 21,509
Modeled Residue Count: 2,692
Deposited Residue Count: 3,064
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-degrading enzyme	A, B	990	Homo sapiens	Mutation(s): 14 Gene Names: IDE, Insulin Degrading Enzyme 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14735
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-bound IDE, heavy chain	C, E	263	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-bound IDE, light chain	D, F	239	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloid beta A4 protein	G, H	40	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067 Go to UniProtKB: P05067
PHAROS: P05067 GTEx: ENSG00000142192
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05067
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.270 (Depositor), 0.270 (DCC)
R-Value Work: 0.228 (Depositor), 0.233 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.583	α = 90
b = 135.324	β = 90
c = 368.524	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASES	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-08-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-08-06
Type: Initial release
Version 1.1: 2014-10-01
Changes: Source and taxonomy
Version 1.2: 2014-10-08
Changes: Derived calculations
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary