8BLU | pdb_00008blu

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 (Depositor), 0.229 (DCC)
R-Value Work:
0.183 (Depositor), 0.191 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8BLU

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
Modeled Residue Count: 774
Deposited Residue Count: 780
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.223 (Depositor), 0.229 (DCC)
R-Value Work: 0.183 (Depositor), 0.191 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.603	α = 90
b = 49.588	β = 93.928
c = 118.194	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-30

Deposition Author(s):

Daniel-Mozo, M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	5U54AG065187-03

Revision History (Full details and data files)

Version 1.0: 2022-11-30
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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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.