3KKA | pdb_00003kka

Co-crystal structure of the sam domains of EPHA1 AND EPHA2

PDB DOI: https://doi.org/10.2210/pdb3KKA/pdb

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

Deposited: 2009-11-05 Released: 2009-11-24
Deposition Author(s): Walker, J.R., Yermekbayeva, L., Butler-Cole, C., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.235 (Depositor), 0.247 (DCC)
R-Value Work:
0.200 (Depositor)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Co-Crystal Structure of the SAM Domains of Human Ephrin Type-A Receptor 1 and Human Ephrin Type-A Receptor 2

Walker, J.R., Yermekbayeva, L., Butler-Cole, C., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Macromolecule Content

Total Structure Weight: 49.35 kDa
Atom Count: 2,562
Modeled Residue Count: 320
Deposited Residue Count: 422
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHRIN TYPE-A RECEPTOR 1	A, B	82	Homo sapiens	Mutation(s): 0 Gene Names: EPH, EPHA1, EPHT, EPHT1, MGC163163 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21709 (Homo sapiens) Explore P21709 Go to UniProtKB: P21709
PHAROS: P21709 GTEx: ENSG00000146904
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21709
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHRIN TYPE-A RECEPTOR 2	C, D, E	86	Homo sapiens	Mutation(s): 0 Gene Names: EPHA2 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens) Explore P29317 Go to UniProtKB: P29317
PHAROS: P29317 GTEx: ENSG00000142627
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29317
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.235 (Depositor), 0.247 (DCC)
R-Value Work: 0.200 (Depositor)
R-Value Observed: 0.202 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.554	α = 90
b = 56.071	β = 90
c = 107.617	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-11-24

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description