3KGP

Crystal Structures of Urokinase-type Plasminogen Activator in Complex with 4-(Aminomethyl) Benzoic Acid and 4-(Aminomethyl-phenyl)-methanol

PDB DOI: https://doi.org/10.2210/pdb3KGP/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2009-10-29 Released: 2009-12-01
Deposition Author(s): Jiang, L.-G., Zhao, G.-X., Bian, X.-B., Yuan, C., Huang, Z.-X., Huang, M.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.274
R-Value Work: 0.199
R-Value Observed: 0.199

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structures of Urokinase-type Plasminogen Activator in Complex with 4-(Aminomethyl) Benzoic Acid and 4-(Aminomethyl-phenyl)-methanol

Jiang, L.-G., Zhao, G.-X., Bian, X.-B., Yuan, C., Huang, Z.-X., Huang, M.-D.

(2009) Chin J Struct Chem 28: 253-259

Macromolecule Content

Total Structure Weight: 28.69 kDa
Atom Count: 2,148
Modelled Residue Count: 239
Deposited Residue Count: 253
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A	253	Homo sapiens	Mutation(s): 2 Gene Names: PLAU EC: 3.4.21.73
UniProt & NIH Common Fund Data Resources
Find proteins for P00749 (Homo sapiens) Explore P00749 Go to UniProtKB: P00749
PHAROS: P00749 GTEx: ENSG00000122861
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00749
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4AZ Query on 4AZ Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-(aminomethyl)benzoic acid C₈ H₉ N O₂ QCTBMLYLENLHLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
4AZ	PDBBind: 3KGP	Ki: 2.68e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.274
R-Value Work: 0.199
R-Value Observed: 0.199
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.834	α = 90
b = 120.834	β = 90
c = 42.488	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-12-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-12-25
Changes: Data collection
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-11-01
Changes: Data collection, Refinement description
Version 1.5: 2024-10-30
Changes: Structure summary

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.