3P8G

Crystal Structure of MT-SP1 in complex with benzamidine

PDB DOI: https://doi.org/10.2210/pdb3P8G/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Saccharomyces cerevisiae
Mutation(s): Yes

Deposited: 2010-10-13 Released: 2011-08-03
Deposition Author(s): Yuan, C., Huang, M., Chen, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.177
R-Value Work: 0.143
R-Value Observed: 0.145

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of catalytic domain of Matriptase in complex with Sunflower trypsin inhibitor-1.

Yuan, C., Chen, L., Meehan, E.J., Daly, N., Craik, D.J., Huang, M., Ngo, J.C.

(2011) BMC Struct Biol 11: 30-30

PubMed: 21693064 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/1472-6807-11-30
Primary Citation of Related Structures:
3P8F, 3P8G

PubMed Abstract:
Matriptase is a type II transmembrane serine protease that is found on the surfaces of epithelial cells and certain cancer cells. Matriptase has been implicated in the degradation of certain extracellular matrix components as well as the activation of various cellular proteins and proteases, including hepatocyte growth factor and urokinase. Sunflower trypsin inhibitor-1 (SFTI-1), a cyclic peptide inhibitor originally isolated from sunflower seeds, exhibits potent inhibitory activity toward matriptase.

Organizational Affiliation

State Key Lab of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China.

Macromolecule Content

Total Structure Weight: 27.44 kDa
Atom Count: 2,293
Modelled Residue Count: 241
Deposited Residue Count: 241
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ST14 protein	A	241	Homo sapiens	Mutation(s): 1 EC: 3.4.21.109
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Y6 (Homo sapiens) Explore Q9Y5Y6 Go to UniProtKB: Q9Y5Y6
PHAROS: Q9Y5Y6 GTEx: ENSG00000149418
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y5Y6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	GLUTATHIONE C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
BEN Query on BEN Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	B [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain D [auth A] Focus chain E [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain C [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	C [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain C [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.177
R-Value Work: 0.143
R-Value Observed: 0.145
Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.888	α = 90
b = 141.701	β = 90
c = 51.995	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-03

Deposition Author(s):

Yuan, C.

Huang, M.

Chen, L.

Revision History (Full details and data files)

Version 1.0: 2011-08-03
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3P8G

Crystal Structure of MT-SP1 in complex with benzamidine

Structure of catalytic domain of Matriptase in complex with Sunflower trypsin inhibitor-1.

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)