Macromolecule Content

Total Structure Weight: 33.61 kDa
Atom Count: 2351
Modelled Residue Count: 272
Deposited Residue Count: 285
Unique protein chains: 1

3ACK

Crystal structure of Pyrrolo pyrazine derivative bound to the kinase domain of human LCK, (auto-phosphorylated on TYR394)

DOI: 10.2210/pdb3ACK/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2010-01-05 Released: 2010-06-30
Deposition Author(s): Tsuji, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.265
R-Value Work: 0.171
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Ab initio fragment molecular orbital study of ligand binding to leukocyte-specific protein tyrosine (LCK) kinase

Ozawa, M., Ozawa, T., Tsuji, E., Okazaki, K., Takeda, K.

To be published.

Macromolecules

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase LCK	A	285	Homo sapiens	Mutation(s): 0 Gene Names: LCK EC: 2.7.10.2
Find proteins for P06239 (Homo sapiens) Explore P06239 Go to UniProtKB: P06239
NIH Common Fund Data Resources
PHAROS: P06239 GTEx: ENSG00000182866
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KSR Query on KSR Download Ideal Coordinates CCD File SDF format, chain E [A] MOL2 format, chain E [A]	A	6-(5-methoxy-1-methyl-1H-indol-3-yl)-5H-pyrrolo[2,3-b]pyrazine C₁₆ H₁₄ N₄ O MIJMZVTYIXYSDK-UHFFFAOYSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [A] SDF format, chain C [A] MOL2 format, chain B [A] MOL2 format, chain C [A]	A	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain D [A] MOL2 format, chain D [A]	A	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PTR	Kd: 400000 nM BindingDB

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.265
R-Value Work: 0.171
R-Value Observed: 0.180
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.224	α = 90
b = 73.714	β = 90
c = 92.22	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2010-01-05
Released Date: 2010-06-30

Deposition Author(s):

Tsuji, E.

Revision History (Full details and data files)

Version 1.0: 2010-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

176528 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

3ACK

Crystal structure of Pyrrolo pyrazine derivative bound to the kinase domain of human LCK, (auto-phosphorylated on TYR394)

Ab initio fragment molecular orbital study of ligand binding to leukocyte-specific protein tyrosine (LCK) kinase

Entity ID: 1

NIH Common Fund Data Resources

Protein Feature View

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)