3T8X

Crystal structure of human CD1b in complex with synthetic antigenic diacylsulfoglycolipid SGL12 and endogenous spacer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural reorganization of the human CD1b Antigen-binding groove for presentation of mycobacterial sulfoglycolipids

Garcia-Alles, L.F.Collmann, A.Versluis, C.Lindner, B.Guiard, J.Maveyraud, L.Huc, E.Im, J.S.Sansano, S.Brando, T.Julien, S.Prandi, J.Gilleron, M.Porcelli, S.A.de la Salle, H.Heck, A.J.R.Mori, L.Puzo, G.Mourey, L.De Libero, G.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1b
A, C
301Homo sapiensMutation(s): 0 
Gene Names: CD1B
Find proteins for P29016 (Homo sapiens)
Go to Gene View: CD1B
Go to UniProtKB:  P29016
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, D
99Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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A, C
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
ULI
Query on ULI

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A, C
tetracontane
n-Tetracontane
C40 H82
KUPLEGDPSCCPJI-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
T8X
Query on T8X

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A, C
2-O-sulfo-alpha-D-glucopyranosyl 2-O-hexadecanoyl-3-O-[(2E,4S,6S,8S)-2,4,6,8-tetramethyltetracos-2-enoyl]-alpha-D-glucopyranoside
2-Palmitoyl-3-[2S,4S,6S,8S-tetramethyl-trans-2-tetracosenoyl]-2'-sulfate-alpha-alpha'-D-trehalose
C56 H104 O16 S
NEVRXHPVRYSQOZ-ZZLYBKFXSA-N
 Ligand Interaction
NAG
Query on NAG

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A, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 203.250α = 90.00
b = 67.580β = 112.26
c = 88.190γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-26
    Type: Initial release