8BLU

The PDZ domains of human SDCBP

PDB DOI: https://doi.org/10.2210/pdb8BLU/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-11-10 Released: 2022-11-30
Deposition Author(s): Bradshaw, W.J., Katis, V.L., Daniel-Mozo, M., 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: 1.50 Å
R-Value Free: 0.223
R-Value Work: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The PDZ domains of human SDCBP

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

To be published.

Macromolecule Content

Total Structure Weight: 87.63 kDa
Atom Count: 7,119
Modelled Residue Count: 774
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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
DGL Query on DGL Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain Y [auth D] MOL2 format, chain L [auth B] MOL2 format, chain Y [auth D] mmCIF format, chain L [auth B] mmCIF format, chain Y [auth D]	L [auth B], Y [auth D]	D-GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-GSVOUGTGSA-N		Interactions Focus chain L [auth B] Focus chain Y [auth D] Interactions & Density Focus chain L [auth B] Focus chain Y [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain W [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain W [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain W [auth D]	G [auth A], K [auth B], W [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain W [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain V [auth D] MOL2 format, chain J [auth B] MOL2 format, chain V [auth D] mmCIF format, chain J [auth B] mmCIF format, chain V [auth D]	J [auth B], V [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain V [auth D] Interactions & Density Focus chain J [auth B] Focus chain V [auth D]
ALA Query on ALA Download Ideal Coordinates CCD File SDF format, chain Z [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain Z [auth D]	Z [auth D]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain Z [auth D] Interactions & Density Focus chain Z [auth D]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	Q [auth C], R [auth C], S [auth C], X [auth D]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D]	E [auth A] F [auth A] H [auth B] I [auth B] N [auth C] E [auth A], F [auth A], H [auth B], I [auth B], N [auth C], O [auth C], P [auth C], T [auth D], U [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Focus chain U [auth D]