5C5B | pdb_00005c5b

Crystal Structure of Human APPL BAR-PH Heterodimer

• PDB DOI: https://doi.org/10.2210/pdb5C5B/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-19 Released: 2016-06-22 
• Deposition Author(s): Chen, Y.J., Chen, B.
• Funding Organization(s): Hong Kong General Research Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.268 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Crystal Structure of Human APPL BAR-PH Heterodimer

Chen, Y.J., Chen, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 171.08 kDa 
• Atom Count: 11,349 
• Modeled Residue Count: 1,457 
• Deposited Residue Count: 1,500 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DCC-interacting protein 13-alpha	A, C	375	Homo sapiens	Mutation(s): 0  Gene Names: APPL1, APPL, DIP13A, KIAA1428
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKG1 (Homo sapiens) Explore Q9UKG1  Go to UniProtKB:  Q9UKG1
PHAROS:  Q9UKG1 GTEx:  ENSG00000157500

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DCC-interacting protein 13-beta	B, D	375	Homo sapiens	Mutation(s): 0  Gene Names: APPL2, DIP13B
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEU8 (Homo sapiens) Explore Q8NEU8  Go to UniProtKB:  Q8NEU8
PHAROS:  Q8NEU8 GTEx:  ENSG00000136044

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth B], G [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.268 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.924	α = 90
b = 88.542	β = 92.65
c = 147.388	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-06-22 
Deposition Author(s): Chen, Y.J., Chen, B.

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Funding Organization	Location	Grant Number
Hong Kong General Research Fund	Hong Kong	HK-GRF 766911

Revision History  

• Version 1.0: 2016-06-22
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description