4AVX | pdb_00004avx

Hepatocyte Growth Factor-Regulated Tyrosine Kinase Substrate (Hgs-Hrs) bound to an IP2 compound at 1.68 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb4AVX/pdb

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


• Deposited: 2012-05-30 Released: 2012-06-13 
• Deposition Author(s): Williams, E., Canning, P., Shrestha, L., Krojer, T., Vollmar, M., Slowey, A., Conway, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Bullock, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.231 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Tandem Vhs and Fyve Domains of Hepatocyte Growth Factor-Regulated Tyrosine Kinase Substrate (Hgs-Hrs) Bound to an Ip2 Compound at 1.68 A Resolution

Williams, E., Canning, P., Shrestha, L., Krojer, T., Vollmar, M., Slowey, A., Conway, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Bullock, A.

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: 27.02 kDa 
• Atom Count: 1,978 
• Modeled Residue Count: 218 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE	A	226	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O14964 (Homo sapiens) Explore O14964  Go to UniProtKB:  O14964
PHAROS:  O14964 GTEx:  ENSG00000185359

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ITP	E [auth A]	PHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5-PHOSPHONOOXY-CYCLOHEXYL) ESTER C6 H14 O12 P2 PUVHMWJJTITUGO-FICORBCRSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	B [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.231 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.825	α = 90
b = 67.545	β = 103.51
c = 57.423	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Williams, E., Canning, P., Shrestha, L., Krojer, T., Vollmar, M., Slowey, A., Conway, S., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Bullock, A.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description