4ZKS | pdb_00004zks

The crystal structure of upain-1-W3A in complex with inactive uPA (uPA-S195A) at pH7.4

PDB DOI: https://doi.org/10.2210/pdb4ZKS/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens, synthetic construct
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2015-04-30 Released: 2016-05-18
Deposition Author(s): Jiang, L., Andreasen, P.A., Huang, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.245 (Depositor), 0.239 (DCC)
R-Value Work:
0.196 (Depositor), 0.195 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4ZKS

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

Literature

The crystal structure of mupain-1-IG in complex with murinised human uPA at pH7.4

Jiang, L., Andreasen, P.A., Huang, M.

To be published.

Macromolecule Content

Total Structure Weight: 29.06 kDa
Atom Count: 2,114
Modeled Residue Count: 258
Deposited Residue Count: 259
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A [auth U]	247	Homo sapiens	Mutation(s): 3 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00749
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
upain-1-W3A	B [auth P]	12	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.245 (Depositor), 0.239 (DCC)
R-Value Work: 0.196 (Depositor), 0.195 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.751	α = 90
b = 120.751	β = 90
c = 42.961	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-05-18

Deposition Author(s):

Andreasen, P.A.

Revision History (Full details and data files)

Version 1.0: 2016-05-18
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Database references, Derived calculations, 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.