2O8U | pdb_00002o8u

Crystal Structure and Binding Epitopes of Urokinase-type Plasminogen Activator (C122A/N145Q/S195A) in complex with Inhibitors

PDB DOI: https://doi.org/10.2210/pdb2O8U/pdb

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

Deposited: 2006-12-12 Released: 2007-12-25
Deposition Author(s): Zhao, G., Yuan, C., Jiang, L., Huang, Z., Huang, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.245 (Depositor), 0.244 (DCC)
R-Value Work:
0.218 (Depositor), 0.218 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2O8U

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

Literature

Crystal Structure and Binding Epitopes of Urokinase-type Plasminogen Activator (C122A/N145Q/S195A) in complex with Inhibitors

Zhao, G., Yuan, C., Jiang, L., Huang, Z., Huang, M.

To be published.

Macromolecule Content

Total Structure Weight: 29.06 kDa
Atom Count: 2,126
Modeled Residue Count: 238
Deposited Residue Count: 253
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase plasminogen activator	A	253	Homo sapiens	Mutation(s): 3 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00749
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
BEN Query on BEN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.245 (Depositor), 0.244 (DCC)
R-Value Work: 0.218 (Depositor), 0.218 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.073	α = 90
b = 120.073	β = 90
c = 42.252	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-12-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-12-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-12-27
Changes: Data collection
Version 1.4: 2024-11-13
Changes: Structure summary

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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.