1SHW

EphB2 / EphrinA5 Complex Structure

PDB DOI: https://doi.org/10.2210/pdb1SHW/pdb

Classification: hormone/growth factor/receptor
Organism(s): Mus musculus
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2004-02-26 Released: 2004-05-18
Deposition Author(s): Himanen, J.P., Chumley, M.J., Lackmann, M., Li, C., Barton, W.A., Jeffrey, P.D., Vearing, C., Geleick, D., Feldheim, D.A., Boyd, A.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.305
R-Value Work: 0.258

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 37.9 kDa
Atom Count: 2,880
Modelled Residue Count: 319
Deposited Residue Count: 319
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin-A5	A	138	Mus musculus	Mutation(s): 0 Gene Names: EFNA5, EPLG7, LERK7, EPL7
UniProt & NIH Common Fund Data Resources
Find proteins for O08543 (Mus musculus) Explore O08543 Go to UniProtKB: O08543
IMPC: MGI:107444
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O08543
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-B receptor 2	B	181	Mus musculus	Mutation(s): 0 Gene Names: EPHB2, EPTH3, NUK, SEK3
UniProt & NIH Common Fund Data Resources
Find proteins for P54763 (Mus musculus) Explore P54763 Go to UniProtKB: P54763
IMPC: MGI:99611
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54763
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation	Interactions Focus chain C
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017 Query on PRD_900017	C	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor		Interactions Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.305
R-Value Work: 0.258
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.89	α = 90
b = 88.97	β = 90
c = 122.81	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-05-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-05-18
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-04-03
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary