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SMTL ID : 8dv4.1 (1 other biounit)

Crystal structure of the BC8B TCR-CD1b-PI complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1:

4 residues within 4Å:

Chain A: T.18, N.19, T.21, W.22

1 PLIP interactions:

1 interactions with chain A

Hydrophobic interactions: A:W.22

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2:

7 residues within 4Å:

Chain A: N.56, F.57, R.167, L.170, G.171
Ligands: MAN.5, GOL.11

1 PLIP interactions:

1 interactions with chain A

Hydrophobic interactions: A:L.170

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3:	2 residues within 4Å: Chain A: K.263, H.264 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.264, A:H.264
EDO.9:	7 residues within 4Å: Chain A: H.10, I.12, W.30, D.32 Chain B: S.55, F.56, Y.63 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4:	1 residues within 4Å: Chain A: K.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.142
GOL.11:	1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.2 No protein-ligand interaction detected (PLIP)

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.5:

3 residues within 4Å:

Chain A: E.163
Ligands: NAG-NAG-BMA-MAN.2, NAG-NAG-BMA-MAN.2

1 PLIP interactions:

1 interactions with chain A

Hydrogen bonds: A:E.163

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6:

1 residues within 4Å:

Chain A: N.127

No protein-ligand interaction detected (PLIP)

1 x CUY: tetracosyl octadecanoate(Non-covalent)

CUY.7:

25 residues within 4Å:

Chain A: V.11, I.12, Q.13, G.27, H.37, W.39, F.48, F.69, Y.72, F.76, V.80, F.83, F.87, M.89, I.95, G.97, I.98, A.99, L.113, R.114, F.122, F.143, L.146, I.147, Y.168

20 PLIP interactions:

20 interactions with chain A

Hydrophobic interactions: A:V.11, A:W.39, A:F.48, A:F.69, A:F.69, A:Y.72, A:F.76, A:V.80, A:F.83, A:F.83, A:F.83, A:F.87, A:I.95, A:A.99, A:F.122, A:F.122, A:F.143, A:L.146, A:I.147, A:Y.168

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8:

4 residues within 4Å:

Chain A: G.232, D.233, L.235, R.245

Ligand excluded by PLIP

3 x NA: SODIUM ION(Non-functional Binders)

NA.10:	2 residues within 4Å: Chain A: E.67, R.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.67
NA.12:	1 residues within 4Å: Chain B: D.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.53
NA.13:	3 residues within 4Å: Chain A: N.237, A.238 Chain B: N.24 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.24, B:N.24, A:A.238 Water bridges: A:N.239

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Farquhar, R. et al., alpha beta T-cell receptor recognition of self-phosphatidylinositol presented by CD1b. J.Biol.Chem. (2023)

Release Date

2023-04-19

Peptides

T-cell surface glycoprotein CD1b: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

T-cell surface glycoprotein CD1b

Beta-2-microglobulin

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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
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Extreme

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