7FSW | pdb_00007fsw

SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z169675004

PDB DOI: https://doi.org/10.2210/pdb7FSW/pdb
Deposition Group: G_1002262 (changed state) ExploreG_1002262

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-01-24 Released: 2023-02-15
Deposition Author(s): Bradshaw, W.J., Katis, V.L., Bountra, C., von Delft, F., Brennan, P.E.
Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.325 (Depositor), 0.330 (DCC)
R-Value Work:
0.247 (Depositor), 0.250 (DCC)
R-Value Observed:
0.251 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

SDCBP PanDDA analysis group deposition

Bradshaw, W.J., Katis, V.L., Bountra, C., von Delft, F., Brennan, P.E.

To be published.

Macromolecule Content

Total Structure Weight: 87.21 kDa
Atom Count: 6,357
Modeled Residue Count: 768
Deposited Residue Count: 780
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Syntenin-1	A, B, C, D	195	Homo sapiens	Mutation(s): 0 Gene Names: SDCBP, MDA9, SYCL
UniProt & NIH Common Fund Data Resources
Find proteins for O00560 (Homo sapiens) Explore O00560 Go to UniProtKB: O00560
PHAROS: O00560 GTEx: ENSG00000137575
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00560
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YDX (Subject of Investigation/LOI) Query on YDX Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	N-(1-methyl-1H-pyrazol-3-yl)-2-(1H-pyrazol-1-yl)acetamide C₉ H₁₁ N₅ O DEBBFOBAIIGVSG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DGL Query on DGL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain T [auth D] MOL2 format, chain I [auth B] MOL2 format, chain T [auth D] mmCIF format, chain I [auth B] mmCIF format, chain T [auth D]	I [auth B], T [auth D]	D-GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-GSVOUGTGSA-N		Interactions Focus chain I [auth B] Focus chain T [auth D] Interactions & Density Focus chain I [auth B] Focus chain T [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	Q [auth D], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain Q [auth D] Focus chain R [auth D]
ALA Query on ALA Download Ideal Coordinates CCD File SDF format, chain S [auth D] MOL2 format, chain S [auth D] mmCIF format, chain S [auth D]	S [auth D]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain S [auth D] Interactions & Density Focus chain S [auth D]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain U [auth D] MOL2 format, chain M [auth C] MOL2 format, chain U [auth D] mmCIF format, chain M [auth C] mmCIF format, chain U [auth D]	M [auth C], U [auth D]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain U [auth D] Interactions & Density Focus chain M [auth C] Focus chain U [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	F [auth A] G [auth B] H [auth B] J [auth C] K [auth C] F [auth A], G [auth B], H [auth B], J [auth C], K [auth C], L [auth C], N [auth D], O [auth D], P [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D]