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), 0.240 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00749
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
upain-1-W3A	B [auth P]	12	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.245 (Depositor), 0.240 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (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

View Full Validation Report

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

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.