SMTL ID : 9ohy.1

CD1c presenting phosphomycoketide in its open conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: V.15, N.16, W.19, Y.85 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.16, A:N.16

1 x 01: (4S,8S,12R,16S,20S)-4,8,12,16,20-pentamethylheptacosyl dihydrogen phosphate

01.2: 28 residues within 4Å: Chain A: F.6, V.8, Q.10, G.22, Q.23, G.24, S.25, H.34, G.35, W.36, S.38, I.43, L.62, L.65, F.66, F.68, Y.69, L.70, A.96, G.97, F.110, V.151, T.154, V.155, L.158, T.162, F.166 Ligands: KZF.5 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:F.6, A:F.6, A:V.8, A:V.8, A:Q.10, A:H.34, A:W.36, A:W.36, A:W.36, A:I.43, A:I.43, A:L.62, A:F.66, A:F.66, A:Y.69, A:Y.69, A:Y.69, A:L.70, A:A.96, A:F.110, A:L.158, A:L.158, A:L.158, A:T.162, A:F.166, A:F.166 Hydrogen bonds: A:L.65

2 x D12: DODECANE(Non-covalent)

D12.3: 10 residues within 4Å: Chain A: Y.69, G.72, L.73, E.76, H.80, S.139, L.143, L.144, Y.148 Ligands: D12.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.73, A:E.76, A:H.80, A:L.143, A:L.144, A:Y.148 D12.4: 10 residues within 4Å: Chain A: Y.69, L.73, I.77, F.90, V.92, F.110, V.112, F.114, L.119 Ligands: D12.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.69, A:L.73, A:I.77, A:F.90, A:V.92, A:F.110, A:V.112, A:L.119

3 x KZF: 2-(cyclohexylazaniumyl)ethanesulfonate(Non-covalent)

KZF.5: 10 residues within 4Å: Chain A: F.12, F.14, A.20, R.21, G.22, S.38, L.70, L.73, T.74 Ligands: 01.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.12, A:F.14, A:F.14, A:A.20, A:L.70, A:L.73, A:T.74 Hydrogen bonds: A:A.20, A:G.22, A:S.38 KZF.6: 11 residues within 4Å: Chain A: L.28, D.29, L.31, L.171, V.178, Y.209, P.210, K.211, P.212, W.240 Ligands: GGG.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.28, A:L.31, A:L.171, A:V.178, A:V.178 Hydrogen bonds: A:D.29, A:D.29, A:K.211 KZF.7: 11 residues within 4Å: Chain A: S.5, H.7, I.9, W.27, D.29, E.30, K.95 Chain B: S.55, F.56, Y.63 Ligands: MLA.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.7, A:I.9, A:W.27, A:K.95 Hydrogen bonds: A:S.5, A:D.29

1 x GGG: glycylglycylglycine(Non-covalent)

GGG.8: 14 residues within 4Å: Chain A: W.27, E.30, L.31, Y.177, R.180, Y.209, P.234, G.238, W.240 Chain B: S.52, Y.63, L.65 Ligands: KZF.6, MLA.10 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.177, A:R.180, B:S.52, B:S.52 Water bridges: A:G.238, A:G.238

2 x MLA: MALONIC ACID(Non-covalent)

MLA.9: 3 residues within 4Å: Chain B: S.57, K.58 Ligands: KZF.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.58 Hydrogen bonds: B:K.58 Water bridges: B:D.59 MLA.10: 5 residues within 4Å: Chain A: N.237 Chain B: H.51, S.52, Y.67 Ligands: GGG.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.237, A:G.238, B:Y.67 Water bridges: B:H.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, T.P. et al., CD1c presenting phosphomycoketide in its open conformation. To Be Published

Release Date

2025-11-19

Peptides

T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein

Beta-2-microglobulin

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