7DZD

Crystal structure of uPA in complex with cleaved camostat

PDB DOI: https://doi.org/10.2210/pdb7DZD/pdb

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

Deposited: 2021-01-25 Released: 2021-07-14
Deposition Author(s): Jiang, L.G., Huang, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 ?
R-Value Free: 0.231
R-Value Work: 0.192
R-Value Observed: 0.194

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of uPA in complex with cleaved camostat

Jiang, L.G., Huang, M.D.

To be published.

Macromolecule Content

Total Structure Weight: 28.07 kDa
Atom Count: 2,063
Modelled Residue Count: 245
Deposited Residue Count: 245
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GBS (Subject of Investigation/LOI) Query on GBS 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]	4-carbamimidamidobenzoic acid C₈ H₉ N₃ O₂ SXTSBZBQQRIYCU-UHFFFAOYSA-N		Interactions Focus chain B [auth U] Interactions & Density Focus chain B [auth U]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain C [auth U] SDF format, chain D [auth U] MOL2 format, chain C [auth U] MOL2 format, chain D [auth U] mmCIF format, chain C [auth U] mmCIF format, chain D [auth U]	C [auth U], D [auth U]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain C [auth U] Focus chain D [auth U] Interactions & Density Focus chain C [auth U] Focus chain D [auth U]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 ?
R-Value Free: 0.231
R-Value Work: 0.192
R-Value Observed: 0.194
Space Group: H 3

Unit Cell:

Length ( ? )	Angle ( ? )
a = 120.317	α = 90
b = 120.317	β = 90
c = 42.451	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data reduction
APEX	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-07-14

Deposition Author(s):

Jiang, L.G.

Huang, M.D.

Revision History (Full details and data files)

Version 1.0: 2021-07-14
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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Help and Resources

7DZD

Crystal structure of uPA in complex with cleaved camostat

Crystal structure of uPA in complex with cleaved camostat

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)