4QT8

Crystal Structure of RON Sema-PSI-IPT1 extracellular domains in complex with MSP beta-chain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage-stimulating protein receptorA [auth B],
B [auth A]
669Homo sapiensMutation(s): 5 
Gene Names: MST1RPTK8RON
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q04912 (Homo sapiens)
Explore Q04912 
Go to UniProtKB:  Q04912
PHAROS:  Q04912
GTEx:  ENSG00000164078 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04912
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor-like protein
C, D
253Homo sapiensMutation(s): 1 
Gene Names: D3F15S2DNF15S2HGFLMSI1MST1
UniProt & NIH Common Fund Data Resources
Find proteins for P26927 (Homo sapiens)
Explore P26927 
Go to UniProtKB:  P26927
PHAROS:  P26927
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26927
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.585α = 90
b = 63.775β = 90.08
c = 146.049γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2015-04-01
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary