8HU2 | pdb_00008hu2

Rattus Syntenin-1 PDZ domain with inhibitor

PDB DOI: https://doi.org/10.2210/pdb8HU2/pdb

Classification: SIGNALING PROTEIN/INHIBITOR
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-12-22 Released: 2024-01-17
Deposition Author(s): Heo, Y., Lee, J., Yun, J.H., Lee, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.234 (Depositor), 0.232 (DCC)
R-Value Work:
0.200 (Depositor)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of STNPDZ with inhibitor at 1.60 Angstroms resolution.

Heo, Y., Lee, J., Yun, J.H., Lee, W.

To be published.

Macromolecule Content

Total Structure Weight: 17.94 kDa
Atom Count: 1,431
Modeled Residue Count: 162
Deposited Residue Count: 163
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Syntenin-1	A	163	Rattus norvegicus	Mutation(s): 0 Gene Names: Sdcbp
UniProt
Find proteins for Q9JI92 (Rattus norvegicus) Explore Q9JI92 Go to UniProtKB: Q9JI92
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9JI92
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M8R (Subject of Investigation/LOI) Query on M8R Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2~{S})-2-(9~{H}-fluoren-9-ylmethoxycarbonylamino)-3-(4-oxidanylidene-5~{H}-pyrimidin-2-yl)propanoic acid C₂₂ H₁₉ N₃ O₅ SRYLOGZQEQKDOT-SFHVURJKSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.234 (Depositor), 0.232 (DCC)
R-Value Work: 0.200 (Depositor)
R-Value Observed: 0.203 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.098	α = 90
b = 71.098	β = 90
c = 73.072	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	model building
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-01-17
Type: Initial release

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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.