7P2D

Structure of alphaMbeta2/Cd11bCD18 headpiece in complex with a nanobody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.262 

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Literature

Structure of the integrin receptor aMb2 headpiece in complex with a function-modulating nanobody

Jensen, R.K.Andersen, G.R.

(null) Submitted Submitted


Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 2 of Integrin alpha-MA763Homo sapiensMutation(s): 0 
Gene Names: ITGAMCD11BCR3A
UniProt & NIH Common Fund Data Resources
Find proteins for P11215 (Homo sapiens)
Explore P11215 
Go to UniProtKB:  P11215
PHAROS:  P11215
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11215
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin betaB473Homo sapiensMutation(s): 0 
Gene Names: ITGB2
UniProt
Find proteins for A0A494C0X7 (Homo sapiens)
Explore A0A494C0X7 
Go to UniProtKB:  A0A494C0X7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A494C0X7
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
hCD11bNb1 nanobodyC129Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD, E, F, G 2N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
J [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.262 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.1α = 90
b = 114.1β = 90
c = 250.12γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR155-2015-2666
Danish Council for Independent ResearchDenmark4181-00137
Novo Nordisk FoundationDenmarkNNF18OC0052105

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release