3RNJ | pdb_00003rnj

Crystal structure of the SH3 domain from IRSp53 (BAIAP2)

• PDB DOI: https://doi.org/10.2210/pdb3RNJ/pdb

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


• Deposited: 2011-04-22 Released: 2011-05-04 
• Deposition Author(s): Simister, P.C., Barilari, M., Muniz, J.R.C., Dente, L., Knapp, S., von Delft, F., Filippakopoulos, P., Vollmar, M., Chaikuad, A., Raynor, J., Tregubova, A., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Feller, S.M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.219 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of the SH3 domain from IRSp53 (BAIAP2)

Simister, P.C., Barilari, M., Muniz, J.R.C., Dente, L., Knapp, S., von Delft, F., Filippakopoulos, P., Vollmar, M., Chaikuad, A., Raynor, J., Tregubova, A., Arrowsmith, C.H., M Edwards, A., Weigelt, J., Bountra, C., Feller, S.M., 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: 8.05 kDa 
• Atom Count: 676 
• Modeled Residue Count: 67 
• Deposited Residue Count: 67 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Brain-specific angiogenesis inhibitor 1-associated protein 2	A	67	Homo sapiens	Mutation(s): 0  Gene Names: BAIAP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQB8 (Homo sapiens) Explore Q9UQB8  Go to UniProtKB:  Q9UQB8
PHAROS:  Q9UQB8 GTEx:  ENSG00000175866

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDT	B [auth A]	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C10 H16 N2 O8 KCXVZYZYPLLWCC-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	F [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.219 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.96	α = 90
b = 36.64	β = 90
c = 58.11	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Simister, P.C., Barilari, M., Muniz, J.R.C., Dente, L., Knapp, S., von Delft, F., Filippakopoulos, P., Vollmar, M., Chaikuad, A., Raynor, J., Tregubova, A., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Feller, S.M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-12-05
  Changes: Database references
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description