8Q6R

Structure of complement FP in complex with the TPP-3077 VHH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structure of complement FP in complex with the TPP-3077 VHH

Andersen, G.R.Pedersen, D.V.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
The properdin specific VHH TPP-3077
A, B
125Lama glamaMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Properdin
C, E
108Homo sapiensMutation(s): 0 
Gene Names: CFP
UniProt & NIH Common Fund Data Resources
Find proteins for P27918 (Homo sapiens)
Explore P27918 
Go to UniProtKB:  P27918
PHAROS:  P27918
GTEx:  ENSG00000126759 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27918
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P27918-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Properdin
D, F
221Homo sapiensMutation(s): 0 
Gene Names: CFP
UniProt & NIH Common Fund Data Resources
Find proteins for P27918 (Homo sapiens)
Explore P27918 
Go to UniProtKB:  P27918
PHAROS:  P27918
GTEx:  ENSG00000126759 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27918
Glycosylation
Glycosylation Sites: 10Go to GlyGen: P27918-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose
G, H, J, K
2O-Glycosylation
Glycosylation Resources
GlyTouCan:  G36855WW
GlyCosmos:  G36855WW
GlyGen:  G36855WW
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCH (Subject of Investigation/LOI)
Query on GCH

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A]
GLYCOCHOLIC ACID
C26 H43 N O6
RFDAIACWWDREDC-FRVQLJSFSA-N
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
DA [auth F]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN (Subject of Investigation/LOI)
Query on MAN

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
CA [auth F]
EA [auth F]
FA [auth F]
AA [auth F],
BA [auth F],
CA [auth F],
EA [auth F],
FA [auth F],
GA [auth F],
HA [auth F],
N [auth C],
O [auth C],
P [auth D],
Q [auth D],
R [auth D],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth D],
X [auth E],
Y [auth E],
Z [auth F]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.21α = 90
b = 63.701β = 103.752
c = 119.249γ = 90
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
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Structure summary