SMTL ID : 8jyc.1

Crystal Structure of Intracellular B30.2 Domain of BTN3A1 and BTN2A1 in Complex with DMAPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: F.33, S.35, S.40, R.42, P.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.33, A:S.40 EDO.8: 3 residues within 4Å: Chain A: E.136, S.137, R.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.137 Water bridges: A:E.136, A:S.137 EDO.11: 3 residues within 4Å: Chain A: D.159, S.161 Chain B: R.211 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.211, A:D.159 Water bridges: B:R.211 EDO.12: 4 residues within 4Å: Chain B: G.120, Y.122, E.136, S.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.120 EDO.13: 7 residues within 4Å: Chain B: F.33, L.34, S.35, S.40, V.41, R.42, P.187 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.40, B:R.42 EDO.14: 3 residues within 4Å: Chain B: P.57, V.98, R.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.98 Water bridges: B:R.100 EDO.17: 4 residues within 4Å: Chain C: K.8, F.12, F.138, Y.149 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.8 EDO.20: 5 residues within 4Å: Chain C: K.9, Y.71, F.138, A.151, G.154 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.9, C:Y.71, C:G.154

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 11 residues within 4Å: Chain A: V.83, E.84, V.86, I.87, M.117, G.120, Y.122, L.134, E.136, S.137, L.138 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.122, A:E.136, A:L.138 1PE.3: 6 residues within 4Å: Chain A: R.95, S.97, P.108, Q.109, N.110, G.111 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.95, A:R.95, A:P.108, A:Q.109 Water bridges: A:A.170 1PE.4: 4 residues within 4Å: Chain A: H.48, L.49, G.50, E.51 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.50 1PE.18: 6 residues within 4Å: Chain B: Q.109, A.170 Chain C: T.100, E.102, N.103, E.121 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.103, C:E.121, C:E.121

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 8 residues within 4Å: Chain A: C.139, R.140, M.157, R.158 Chain B: C.139, R.140, M.157, R.158 No protein-ligand interaction detected (PLIP) PG4.6: 9 residues within 4Å: Chain A: Q.63, E.103, V.104, L.105, L.106, E.116, H.118, R.123, R.180 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.118, A:R.180, A:R.180, A:R.180 PG4.19: 5 residues within 4Å: Chain A: T.201, P.203 Chain C: T.111, D.112, K.115 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.112, C:K.115 Water bridges: C:R.117

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 5 residues within 4Å: Chain A: E.84, N.85, I.87, E.184, S.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.186

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 5 residues within 4Å: Chain B: P.25, D.26, E.36, R.38, R.59 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.26, B:D.26, B:R.38, B:R.59 PEG.10: 7 residues within 4Å: Chain B: R.43, S.62, P.64, E.88, R.180, G.182 Ligands: PEG.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.88, B:R.180, B:R.180 PEG.15: 5 residues within 4Å: Chain B: H.29, D.31, R.43, P.64 Ligands: PEG.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.43

2 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)

DMA.16: 13 residues within 4Å: Chain A: G.199, V.200, T.201, V.202 Chain B: R.168 Chain C: W.55, H.56, Y.57, W.96, R.117, R.123, R.174, L.176 15 PLIP interactions: 13 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:W.55, C:W.55, C:Y.57, C:L.176, C:L.176 Hydrogen bonds: C:W.96, C:R.174, A:V.202 Water bridges: C:R.117, C:R.123, C:R.123 Salt bridges: C:R.117, C:R.123, C:R.174, B:R.168 DMA.21: 14 residues within 4Å: Chain A: R.168 Chain B: G.199, V.200, T.201, V.202 Chain D: W.55, H.56, Y.57, W.96, R.117, L.119, R.123, R.174, L.176 13 PLIP interactions: 10 interactions with chain D, 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: D:W.55, D:W.55, D:L.176, D:L.176 Hydrogen bonds: D:R.174, B:T.201, B:V.202 Water bridges: D:R.123, D:R.123 Salt bridges: D:R.117, D:R.123, D:R.174, A:R.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, L. et al., Phosphoantigens glue butyrophilin 3A1 and 2A1 to activate V gamma 9V delta 2 T cells. Nature (2023)

Release Date

2023-09-13

Peptides

Butyrophilin subfamily 2 member A1: AB
Butyrophilin subfamily 3 member A1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Butyrophilin subfamily 2 member A1

Butyrophilin subfamily 3 member A1

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