4IC0 | pdb_00004ic0

Crystal Structure of PAI-1 in Complex with Gallate

PDB DOI: https://doi.org/10.2210/pdb4IC0/pdb

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

Deposited: 2012-12-09 Released: 2013-12-11
Deposition Author(s): Hong, Z.B., Lin, Z.H., Gong, L.H., Huang, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.202 (Depositor), 0.210 (DCC)
R-Value Observed:
0.205 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of PAI-1 in Complex with Gallate

Hong, Z.B., Lin, Z.H., Gong, L.H., Huang, M.D.

To be published.

Macromolecule Content

Total Structure Weight: 171.52 kDa
Atom Count: 11,613
Modeled Residue Count: 1,449
Deposited Residue Count: 1,516
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasminogen activator inhibitor 1	A, B, C, D	379	Homo sapiens	Mutation(s): 5 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05121
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDE Query on GDE Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth C]	E [auth A], F [auth C]	3,4,5-trihydroxybenzoic acid C₇ H₆ O₅ LNTHITQWFMADLM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
GDE	BindingDB: 4IC0	IC50: 6600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.258 (Depositor), 0.260 (DCC)
R-Value Work: 0.202 (Depositor), 0.210 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.28	α = 90.91
b = 74.99	β = 93.29
c = 103.873	γ = 115.82

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-12-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-12-11
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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.