6RLO

Crystal structure of AT1412dm Fab fragment in complex with CD9 large extracellular loop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of a homo-dimerization site in tetraspanin CD9 targeted by a melanoma patient-derived antibody

Neviani, V.Pos, W.Schotte, R.Wagner, K.Go, D.M.Fatmawati, C.Kedde, M.Claassen, Y.B.Kroon-Batenburg, L.Lutz, M.Verdegaal, E.M.E.van der Burg, S.H.Spits, H.Gros, P.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AT1412dm Fab Fragment (Heavy Chain)A,
D [auth C],
G [auth E],
J [auth G]
223Homo sapiensMutation(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
AT1412dm Fab Fragment (Light Chain)B,
E [auth D],
H [auth F],
K [auth H]
220Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CD9 antigenC [auth I],
F [auth J],
I [auth K],
L
90Homo sapiensMutation(s): 0 
Gene Names: CD9MIC3TSPAN29GIG2
UniProt & NIH Common Fund Data Resources
Find proteins for P21926 (Homo sapiens)
Explore P21926 
Go to UniProtKB:  P21926
PHAROS:  P21926
GTEx:  ENSG00000010278 
Entity Groups  
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UniProt GroupP21926
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
P [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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BA [auth F]
DA [auth G]
EA [auth H]
M [auth A]
N [auth A]
BA [auth F],
DA [auth G],
EA [auth H],
M [auth A],
N [auth A],
O [auth B],
R [auth I],
S [auth C],
T [auth C],
W [auth D],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth D]
CA [auth F]
Q [auth B]
U [auth C]
V [auth C]
AA [auth D],
CA [auth F],
Q [auth B],
U [auth C],
V [auth C],
Y [auth D],
Z [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.776α = 71.12
b = 89.858β = 89.59
c = 91.533γ = 85.96
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific ResearchNetherlands024.002.009

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary