3DKO | pdb_00003dko

Complex between the kinase domain of human ephrin type-a receptor 7 (epha7) and inhibitor alw-ii-49-7

PDB DOI: https://doi.org/10.2210/pdb3DKO/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-25 Released: 2008-08-19
Deposition Author(s): Walker, J.R., Syeda, F., Gray, N., Butler-Cole, C., Bountra, C., Wolkstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.232 (Depositor), 0.224 (DCC)
R-Value Work:
0.189 (Depositor)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Kinase domain of human ephrin type-a receptor 7 (epha7) in complex with ALW-II-49-7

Walker, J.R., Syeda, F., Gray, N., Butler-Cole, C., Bountra, C., Wolkstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Macromolecule Content

Total Structure Weight: 36.65 kDa
Atom Count: 2,358
Modeled Residue Count: 275
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 7	A	318	Homo sapiens	Mutation(s): 0 Gene Names: EPHA7, EHK3, HEK11 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15375 (Homo sapiens) Explore Q15375 Go to UniProtKB: Q15375
PHAROS: Q15375 GTEx: ENSG00000135333
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15375
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IHZ Query on IHZ 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]	5-[(2-methyl-5-{[3-(trifluoromethyl)phenyl]carbamoyl}phenyl)amino]pyridine-3-carboxamide C₂₁ H₁₇ F₃ N₄ O₂ SAAYRHKJHDIDPH-UHFFFAOYSA-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: 0.232 (Depositor), 0.224 (DCC)
R-Value Work: 0.189 (Depositor)
R-Value Observed: 0.191 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.658	α = 90
b = 52.658	β = 90
c = 217.059	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-08-19

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-08-19
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