7FT0

SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z56767614


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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.

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
RWP (Subject of Investigation/LOI)
Query on RWP

Download Ideal Coordinates CCD File 
J [auth C]methyl 4-[(trifluoroacetyl)amino]benzoate
C10 H8 F3 N O3
MDDVOSSRTNAXHJ-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
O [auth D]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
DGL
Query on DGL

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I [auth B],
V [auth D]
D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
R [auth D],
S [auth D],
T [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ALA
Query on ALA

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

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N [auth C],
W [auth D]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
G [auth B]
H [auth B]
K [auth C]
L [auth C]
E [auth A],
G [auth B],
H [auth B],
K [auth C],
L [auth C],
M [auth C],
P [auth D],
Q [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.894α = 90
b = 49.566β = 94.949
c = 115.233γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2023-02-15
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection