2QYQ | pdb_00002qyq

Human raf kinase inhibitor protein (rkip) in complex with o-phosphotyrosine

• PDB DOI: https://doi.org/10.2210/pdb2QYQ/pdb

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


• Deposited: 2007-08-15 Released: 2008-07-15 
• Deposition Author(s): Simister, P.C., Brady, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.208 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Phosphotyrosine recognition by the Raf Kinase Inhibitor Protein

Simister, P.C., Burton, N.M., Brady, R.L.

(2011) For Immunopathol Dis Therap 2: 59-70

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: 21.35 kDa 
• Atom Count: 1,659 
• Modeled Residue Count: 186 
• Deposited Residue Count: 187 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylethanolamine-binding protein 1	A	187	Homo sapiens	Mutation(s): 0  Gene Names: PEBP1, PBP, PEBP
UniProt & NIH Common Fund Data Resources
Find proteins for P30086 (Homo sapiens) Explore P30086  Go to UniProtKB:  P30086
PHAROS:  P30086 GTEx:  ENSG00000089220

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTR	B [auth A]	O-PHOSPHOTYROSINE C9 H12 N O6 P DCWXELXMIBXGTH-QMMMGPOBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.208 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.674	α = 90
b = 33.892	β = 96.09
c = 59.705	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Simister, P.C., Brady, R.L.

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection