8BLV | pdb_00008blv

The PDZ domains of human SDCBP with a bound SDC4 C-terminal peptide

• PDB DOI: https://doi.org/10.2210/pdb8BLV/pdb

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


• Deposited: 2022-11-10 Released: 2022-12-21 
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.222 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.191 (DCC) 

Starting Model: experimental

Literature

The PDZ domains of human SDCBP with a bound SDC4 C-terminal peptide

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.22 kDa 
• Atom Count: 3,432 
• Modeled Residue Count: 384 
• Deposited Residue Count: 406 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Syntenin-1	A, B	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Syndecan-4	C, D	8	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P31431 (Homo sapiens) Explore P31431  Go to UniProtKB:  P31431
PHAROS:  P31431 GTEx:  ENSG00000124145

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A], H [auth A], J [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.222 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.191 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.71	α = 90
b = 67.462	β = 90
c = 106.74	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-21 
Deposition Author(s): Bradshaw, W.J., Katis, V.L., Daniel-Mozo, M., Bountra, C., von Delft, F., Brennan, P.E.

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

Revision History  

• Version 1.0: 2022-12-21
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description