3MX0
Crystal Structure of EphA2 ectodomain in complex with ephrin-A5
- PDB DOI: https://doi.org/10.2210/pdb3MX0/pdb
- Classification: TRANSFERASE RECEPTOR/SIGNALLING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2010-05-06 Released: 2010-06-30 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.51 Å
- R-Value Free: 0.295 
- R-Value Work: 0.234 
- R-Value Observed: 0.237 
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Ephrin type-A receptor 2 | 409 | Homo sapiens | Mutation(s): 0  Gene Names: EPHA2, ECK 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P29317 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Ephrin-A5 | 138 | Homo sapiens | Mutation(s): 0  Gene Names: EFNA5, EPLG7, LERK7 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P52803 (Homo sapiens) Explore P52803  Go to UniProtKB:  P52803 | |||||
PHAROS:  P52803 GTEx:  ENSG00000184349  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P52803 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 | E, F | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | G [auth A], H [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
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 | E, F | triacetyl-beta-chitotriose | Oligosaccharide / Inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.51 Å
- R-Value Free: 0.295 
- R-Value Work: 0.234 
- R-Value Observed: 0.237 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 57.859 | α = 90 |
b = 89.049 | β = 96.22 |
c = 198.15 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
PHENIX | phasing |
Entry History 
Deposition Data
- Released Date: 2010-06-30  Deposition Author(s): Himanen, J.P., Yermekbayeva, L., Janes, P.W., Walker, J.R., Xu, K., Atapattu, L., Rajashankar, K.R., Mensinga, A., Lackmann, M., Nikolov, D.B., Dhe-Paganon, S.
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 - Version 1.2: 2017-11-08
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary