5Z1C | pdb_00005z1c

The crystal structure of uPA in complex with 4-Iodobenzylamine at pH7.4

PDB DOI: https://doi.org/10.2210/pdb5Z1C/pdb

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

Deposited: 2017-12-25 Released: 2018-12-26
Deposition Author(s): Jiang, L.G., Zhang, X., Luo, Z.P., Huang, M.D.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.143 (Depositor), 0.150 (DCC)
R-Value Work:
0.118 (Depositor), 0.123 (DCC)
R-Value Observed:
0.119 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases

Jiang, L.G., Zhang, X., Zhou, Y., Chen, Y.Y., Luo, Z.P., Li, J.Y., Yuan, C., Huang, M.D.

(2018) RSC Adv 49: 28189-28197

DOI: https://doi.org/10.1039/c8ra03145b

Macromolecule Content

Total Structure Weight: 27.82 kDa
Atom Count: 2,138
Modeled Residue Count: 245
Deposited Residue Count: 245
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A [auth U]	245	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00749
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZXI Query on ZXI Download:Ideal Coordinates CCD File SDF format, chain B [auth U] MOL2 format, chain B [auth U] mmCIF format, chain B [auth U]	B [auth U]	1-(4-iodophenyl)methanamine C₇ H₈ I N KCGZGJOBKAXVSU-UHFFFAOYSA-N		Interactions Focus chain B [auth U] Interactions & Density Focus chain B [auth U]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.143 (Depositor), 0.150 (DCC)
R-Value Work: 0.118 (Depositor), 0.123 (DCC)
R-Value Observed: 0.119 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.503	α = 90
b = 120.503	β = 90
c = 42.719	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-12-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31400637
National Natural Science Foundation of China	China	31170707
National Natural Science Foundation of China	China	31370737

Revision History (Full details and data files)

Version 1.0: 2018-12-26
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
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.