5WXR

Crystal structure of uPA in complex with upain-2-4-W3A

PDB DOI: https://doi.org/10.2210/pdb5WXR/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens, Phage display vector pTDisp
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2017-01-08 Released: 2018-07-11
Deposition Author(s): Jiang, L., Huang, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.234
R-Value Work: 0.194
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of uPA in complex with upain-2-4-W3A

Jiang, L., Huang, M.

To be published.

Macromolecule Content

Total Structure Weight: 29.8 kDa
Atom Count: 2,131
Modelled Residue Count: 259
Deposited Residue Count: 267
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 chain B	A [auth U]	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
upain-2-4-W3A peptide	B [auth P]	14	Phage display vector pTDisp	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: 1.75 Å
R-Value Free: 0.234
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.874	α = 90
b = 120.874	β = 90
c = 42.958	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-07-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-07-11
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.