3UT3 | pdb_00003ut3

A novel PAI-I inhibitor and its structural mechanism

PDB DOI: https://doi.org/10.2210/pdb3UT3/pdb

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

Deposited: 2011-11-25 Released: 2013-02-06
Deposition Author(s): Lin, Z.H., Hong, Z.B., Shi, X.L., Hu, L.H., Andreasen, P.A., Huang, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.245 (Depositor), 0.244 (DCC)
R-Value Work:
0.202 (Depositor), 0.206 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A novel PAI-I inhibitor and its structural mechanism

Lin, Z.H., Hong, Z.B., Shi, X.L., Hu, L.H., Andreasen, P.A., Huang, M.D.

To be published.

Macromolecule Content

Total Structure Weight: 169.53 kDa
Atom Count: 11,638
Modeled Residue Count: 1,455
Deposited Residue Count: 1,500
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasminogen activator inhibitor 1	A, B, C, D	375	Homo sapiens	Mutation(s): 4 Gene Names: SERPINE1, PAI1, PLANH1
UniProt & NIH Common Fund Data Resources
Find proteins for P05121 (Homo sapiens) Explore P05121 Go to UniProtKB: P05121
PHAROS: P05121 GTEx: ENSG00000106366
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05121
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EMJ Query on EMJ Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	2,5-dihydroxy-3-undecylcyclohexa-2,5-diene-1,4-dione C₁₇ H₂₆ O₄ IRSFLDGTOHBADP-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.245 (Depositor), 0.244 (DCC)
R-Value Work: 0.202 (Depositor), 0.206 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.252	α = 90.89
b = 74.953	β = 93.33
c = 103.775	γ = 115.72

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-02-06

Deposition Author(s):

Andreasen, P.A.

Revision History (Full details and data files)

Version 1.0: 2013-02-06
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.