8BLU

The PDZ domains of human SDCBP


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Syntenin-1
A, B, C, D
195Homo sapiensMutation(s): 0 
Gene Names: SDCBPMDA9SYCL
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00560
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
M [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
DGL
Query on DGL

Download Ideal Coordinates CCD File 
L [auth B],
Y [auth D]
D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
W [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth B],
V [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ALA
Query on ALA

Download Ideal Coordinates CCD File 
Z [auth D]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
GLY
Query on GLY

Download Ideal Coordinates CCD File 
Q [auth C],
R [auth C],
S [auth C],
X [auth D]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.603α = 90
b = 49.588β = 93.928
c = 118.194γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United States5U54AG065187-03

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