SMTL ID : 6oor.1

Structure of 1B1 bound to mouse CD1d

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NA.1: 7 residues within 4Å: Chain A: E.97, I.98, Q.99, A.119, F.120, Q.121, G.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.99, A:Q.99, A:G.122 NA.2: 5 residues within 4Å: Chain A: W.133, L.150, D.153, T.156, S.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.133 NA.6: 6 residues within 4Å: Chain C: H.36, Y.37, L.38, H.55 Chain D: W.112 Ligands: NA.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.38, C:H.55 NA.7: 7 residues within 4Å: Chain C: Y.37, L.38, S.39, L.94, T.96 Chain D: W.112 Ligands: NA.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.37, C:T.96

3 x UNL: UNKNOWN LIGAND

UNL.3: 7 residues within 4Å: Chain A: S.76, V.118, L.143, L.150, T.156 Chain D: G.105, L.106 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.106, A:V.118, A:L.143, A:L.150 UNL.4: 15 residues within 4Å: Chain A: S.12, Q.14, S.28, V.30, W.40, L.66, F.70, Y.73, A.102, G.103, L.163, T.167, C.168, F.171 Ligands: UNL.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Q.14, A:V.30, A:W.40, A:L.66, A:F.70, A:F.70, A:Y.73, A:A.102, A:L.163, A:T.167, A:F.171 UNL.5: 5 residues within 4Å: Chain A: H.68, M.69, V.72, Y.73 Ligands: UNL.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.72, A:Y.73, A:Y.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ying, G. et al., Structural basis of NKT cell inhibition using the T-cell receptor-blocking anti-CD1d antibody 1B1. J.Biol.Chem. (2019)

Release Date

2019-07-17

Peptides

Antigen-presenting glycoprotein CD1d1: A
Beta-2-microglobulin: B
Antibody 1B1 Light chain: C
Antibody 1B1 Heavy chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
L

D
H

Antigen-presenting glycoprotein CD1d1

Beta-2-microglobulin

Antibody 1B1 Light chain

Antibody 1B1 Heavy chain

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