4TRY | pdb_00004try

Structure of BACE1 complex with a HEA-type inhibitor

PDB DOI: https://doi.org/10.2210/pdb4TRY/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-06-18 Released: 2015-07-29
Deposition Author(s): Akaji, K., Teruya, K., Akiyama, T., Sanjho, A., Yamashita, E., Nakagawa, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.252 (Depositor), 0.262 (DCC)
R-Value Work:
0.179 (Depositor), 0.206 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Structure of BACE1 complex with an anti-HMC-type inhibitor

Akaji, K., Teruya, K., Akiyama, T., Sanjho, A., Yamashita, E., Nakagawa, A.

To be published.

Macromolecule Content

Total Structure Weight: 131.93 kDa
Atom Count: 9,326
Modeled Residue Count: 1,175
Deposited Residue Count: 1,176
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	388	Homo sapiens	Mutation(s): 0 Gene Names: BACE1, BACE, KIAA1149 EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens) Explore P56817 Go to UniProtKB: P56817
PHAROS: P56817 GTEx: ENSG00000186318
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P56817
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLU-ILE-TIH-THC-NVA	D, E, F	4	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TIH Query on TIH	D, E, F	L-PEPTIDE LINKING	C₇ H₉ N O₂ S		ALA

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002106 Query on PRD_002106	D, E, F	syn-HEA type inhibitor	Peptide-like / Enzyme inhibitor		Interactions Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain D Focus chain E Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.252 (Depositor), 0.262 (DCC)
R-Value Work: 0.179 (Depositor), 0.206 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.326	α = 90
b = 102.618	β = 103.53
c = 101.287	γ = 90

Software Package:

Software Name	Purpose
DENZO	data collection
SCALEPACK	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	model building
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-07-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-29
Type: Initial release
Version 1.1: 2020-01-29
Changes: Data collection, Derived calculations, Source and taxonomy
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.