1BKM

COCRYSTAL STRUCTURE OF D-AMINO ACID SUBSTITUTED PHOSPHOPEPTIDE COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1BKM/pdb

• Classification: TRANSFORMING PROTEIN
• Organism(s): Rous sarcoma virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-05-02 Released: 1997-07-07 
• Deposition Author(s): Holland, D.R., Rubin, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.275 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Structure-Based Design of a Novel Series of Nonpeptide Ligands that Bind to the Pp60Src Sh2 Domain

Holland, D.R., Lunney, E.A., Plummer, M.S., Mueller, W.T., Mcconnell, P., Pavlovsky, A., Para, K.S., Shahripour, A., Humblet, C., Sawyer, T.K., Rubin, J.R.

(1997) J Am Chem Soc 119: 12471

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.42 kDa 
• Atom Count: 914 
• Modelled Residue Count: 102 
• Deposited Residue Count: 113 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PP60 V-SRC TYROSINE KINASE TRANSFORMING PROTEIN	A	113	Rous sarcoma virus	Mutation(s): 0  EC: 2.7.1.112
UniProt
Find proteins for P00524 (Rous sarcoma virus subgroup A (strain Schmidt-Ruppin)) Explore P00524  Go to UniProtKB:  P00524

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1C5	B [auth A]	[[O-PHOSPHONO-N-ACETYL-TYROSINYL]-GLUTAMYL-3[CYCLOHEXYLMETHYL]ALANINYL]-AMINE C26 H39 N4 O10 P MYZLOAXXVDGNMQ-FSSWDIPSSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1C5	PDBBind:  1BKM	IC50: 1800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.275 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.2	α = 90
b = 46.9	β = 90
c = 74.52	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
XDS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-07-07 
Deposition Author(s): Holland, D.R., Rubin, J.R.

Revision History  

• Version 1.0: 1997-07-07
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection