3T7L | pdb_00003t7l

Crystal structure of the FYVE domain of endofin (ZFYVE16) at 1.1A resolution

• PDB DOI: https://doi.org/10.2210/pdb3T7L/pdb

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


• Deposited: 2011-07-30 Released: 2011-08-31 
• Deposition Author(s): Chaikuad, A., Williams, E., Guo, K., Sanvitale, C., Berridge, G., Krojer, T., Muniz, J.R.C., Canning, P., Phillips, C., Shrestha, A., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.09 Å
• R-Value Free: 
  0.154 (Depositor), 0.157 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Literature

Crystal structure of the FYVE domain of endofin (ZFYVE16) at 1.1A resolution

Chaikuad, A., Williams, E., Guo, K., Sanvitale, C., Berridge, G., Krojer, T., Muniz, J.R.C., Canning, P., Phillips, C., Shrestha, A., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 10.44 kDa 
• Atom Count: 745 
• Modeled Residue Count: 74 
• Deposited Residue Count: 90 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger FYVE domain-containing protein 16	A	90	Homo sapiens	Mutation(s): 0  Gene Names: KIAA0305, ZFYVE16
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z3T8 (Homo sapiens) Explore Q7Z3T8  Go to UniProtKB:  Q7Z3T8
PHAROS:  Q7Z3T8 GTEx:  ENSG00000039319

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.09 Å
• R-Value Free:  0.154 (Depositor), 0.157 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.944	α = 90
b = 42.944	β = 90
c = 76.879	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
SHARP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Chaikuad, A., Williams, E., Guo, K., Sanvitale, C., Berridge, G., Krojer, T., Muniz, J.R.C., Canning, P., Phillips, C., Shrestha, A., von Delft, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations