SMTL ID : 6v7y.1

Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: W.20, T.21, R.22, N.39, D.40 No protein-ligand interaction detected (PLIP)

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.2: 3 residues within 4Å: Chain A: A.16, N.17, W.20 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.105 Ligands: CL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.105 NAG.6: 4 residues within 4Å: Chain A: G.125, T.126, Q.156, N.160 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.156, A:N.160 Water bridges: A:N.109, A:N.109

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: P.196, G.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.197 SO4.11: 3 residues within 4Å: Chain B: S.58, K.59, D.60 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:R.8 Hydrogen bonds: B:S.58, B:K.59, B:D.60 SO4.12: 2 residues within 4Å: Chain B: R.4, T.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.5, B:T.5 Salt bridges: B:R.4 SO4.13: 4 residues within 4Å: Chain B: K.42, F.71, T.72, Y.79 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.72, B:Y.79 Water bridges: B:K.42, B:K.42 Salt bridges: B:K.42 SO4.14: 3 residues within 4Å: Chain B: I.47, E.48, K.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.48, B:K.49

1 x AGH: N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE(Non-covalent)

AGH.5: 32 residues within 4Å: Chain A: L.7, C.9, L.10, L.26, A.27, H.35, W.37, V.44, W.60, F.67, Y.70, S.73, F.74, D.77, V.78, F.81, L.87, A.97, W.128, L.145, D.148, W.150, T.151, T.154, V.155, L.158, L.159, T.162, C.163, F.166 Chain C: R.115, Y.116 34 PLIP interactions: 30 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.7, A:A.27, A:W.37, A:V.44, A:W.60, A:W.60, A:F.67, A:F.67, A:Y.70, A:Y.70, A:Y.70, A:F.74, A:F.74, A:V.78, A:F.81, A:L.87, A:A.97, A:W.128, A:L.145, A:T.151, A:T.154, A:L.158, A:L.158, A:L.159, A:T.162, A:F.166, A:F.166 Water bridges: A:D.148, A:D.148, A:T.151, C:R.99, C:R.99 Hydrogen bonds: C:R.115, C:Y.116

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

CL.7: 1 residues within 4Å: Chain A: H.112 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: G.104 Ligands: NAG.3 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: P.192, S.193 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: S.41, D.42 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: R.46 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shahine, A. et al., A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response. Nat Cancer (2020)

Release Date

2020-09-16

Peptides

Antigen-presenting glycoprotein CD1d: A
Beta-2-microglobulin: B
Nanobody VHH ID5: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

Antigen-presenting glycoprotein CD1d

Beta-2-microglobulin

Nanobody VHH ID5

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