1BKM | pdb_00001bkm

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.275 (Depositor)
R-Value Work:
0.200 (Depositor), 0.255 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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

Macromolecule Content

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

Macromolecules

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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 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt
Find proteins for P00524 (Rous sarcoma virus subgroup A (strain Schmidt-Ruppin)) Explore P00524 Go to UniProtKB: P00524
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00524
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1C5 Query on 1C5 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	[[O-PHOSPHONO-N-ACETYL-TYROSINYL]-GLUTAMYL-3[CYCLOHEXYLMETHYL]ALANINYL]-AMINE C₂₆ H₃₉ N₄ O₁₀ P MYZLOAXXVDGNMQ-FSSWDIPSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.275 (Depositor)
R-Value Work: 0.200 (Depositor), 0.255 (DCC)
R-Value Observed: 0.200 (Depositor)

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

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Entry History

Deposition Data

Released Date: 1997-07-07

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.