4J9G | pdb_00004j9g

Crystal structure of the ABL-SH3 domain complexed with the designed high-affinity peptide ligand P7 at pH7

PDB DOI: https://doi.org/10.2210/pdb4J9G/pdb

Classification: Transferase/unknown function
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-02-16 Released: 2014-01-29
Deposition Author(s): Camara-Artigas, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.244 (Depositor), 0.246 (DCC)
R-Value Work:
0.206 (Depositor), 0.214 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the ABL-SH3 domain complexed with the designed high-affinity peptide ligand P7

Camara-Artigas, A.

To be published.

Macromolecule Content

Total Structure Weight: 24.39 kDa
Atom Count: 1,695
Modeled Residue Count: 205
Deposited Residue Count: 222
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase ABL1	A, C, E	63	Homo sapiens	Mutation(s): 0 Gene Names: ABL, ABL1, JTK7 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P00519 (Homo sapiens) Explore P00519 Go to UniProtKB: P00519
PHAROS: P00519 GTEx: ENSG00000097007
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00519
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P7	B, D, F	11	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth E] MOL2 format, chain G [auth E] mmCIF format, chain G [auth E]	G [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth E] Interactions & Density Focus chain G [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth E] MOL2 format, chain H [auth E] mmCIF format, chain H [auth E]	H [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth E] Interactions & Density Focus chain H [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.244 (Depositor), 0.246 (DCC)
R-Value Work: 0.206 (Depositor), 0.214 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.309	α = 90
b = 86.309	β = 90
c = 45.236	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-01-29

Deposition Author(s):

Camara-Artigas, A.

Revision History (Full details and data files)

Version 1.0: 2014-01-29
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-27
Changes: Structure summary

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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.