SMTL ID : 8qfe.1

Cryogenic crystal structure of the Photoactivated Adenylate Cyclase OaPAC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-hexamer

Ligands

6 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 18 residues within 4Å: Chain A: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.22, A:I.22, A:L.39, A:F.46 Hydrogen bonds: A:K.29, A:N.30, A:N.30, A:Q.48, A:D.67, A:D.67, A:R.69 Water bridges: A:R.63 Salt bridges: A:K.29 FMN.3: 94 residues within 4Å: Chain B: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain C: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain D: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain E: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain F: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Ligands: FMN.5, FMN.7, FMN.9, FMN.11 76 PLIP interactions: 9 interactions with chain E, 34 interactions with chain B, 9 interactions with chain D, 11 interactions with chain C, 13 interactions with chain F Hydrogen bonds: E:S.26, E:K.29, E:N.30, E:N.30, E:Q.48, E:R.63, E:I.64, E:R.69, B:S.26, B:K.29, B:N.30, B:N.30, B:N.30, B:Q.48, B:R.63, B:R.63, B:I.64, B:D.67, B:R.69, B:R.69, D:K.29, D:N.30, D:Q.48, D:Q.48, D:R.63, D:I.64, D:D.67, D:R.69, C:S.26, C:K.29, C:N.30, C:Q.48, C:R.63, C:R.63, C:I.64, C:D.67, C:R.69, F:S.26, F:K.29, F:N.30, F:Q.48, F:R.63, F:R.63, F:R.69 Salt bridges: E:K.29, B:K.29, D:K.29, C:K.29, F:K.29 Hydrophobic interactions: B:I.22, B:I.22, B:L.39, B:F.46, B:Q.48, B:H.70, C:D.67 Water bridges: B:N.30, B:N.30, B:N.30, B:N.30, B:N.30, B:R.63, B:R.63, B:R.63, B:R.63, B:R.63, B:R.69, B:R.69, B:R.69, B:R.69, B:R.69, F:N.30, F:N.30, F:N.30, F:N.30, F:N.30 FMN.5: 94 residues within 4Å: Chain B: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain C: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain D: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain E: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain F: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Ligands: FMN.3, FMN.7, FMN.9, FMN.11 76 PLIP interactions: 9 interactions with chain E, 34 interactions with chain B, 9 interactions with chain D, 11 interactions with chain C, 13 interactions with chain F Hydrogen bonds: E:S.26, E:K.29, E:N.30, E:N.30, E:Q.48, E:R.63, E:I.64, E:R.69, B:S.26, B:K.29, B:N.30, B:N.30, B:N.30, B:Q.48, B:R.63, B:R.63, B:I.64, B:D.67, B:R.69, B:R.69, D:K.29, D:N.30, D:Q.48, D:Q.48, D:R.63, D:I.64, D:D.67, D:R.69, C:S.26, C:K.29, C:N.30, C:Q.48, C:R.63, C:R.63, C:I.64, C:D.67, C:R.69, F:S.26, F:K.29, F:N.30, F:Q.48, F:R.63, F:R.63, F:R.69 Salt bridges: E:K.29, B:K.29, D:K.29, C:K.29, F:K.29 Hydrophobic interactions: B:I.22, B:I.22, B:L.39, B:F.46, B:Q.48, B:H.70, C:D.67 Water bridges: B:N.30, B:N.30, B:N.30, B:N.30, B:N.30, B:R.63, B:R.63, B:R.63, B:R.63, B:R.63, B:R.69, B:R.69, B:R.69, B:R.69, B:R.69, F:N.30, F:N.30, F:N.30, F:N.30, F:N.30 FMN.7: 94 residues within 4Å: Chain B: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain C: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain D: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain E: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain F: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Ligands: FMN.3, FMN.5, FMN.9, FMN.11 76 PLIP interactions: 9 interactions with chain E, 34 interactions with chain B, 9 interactions with chain D, 11 interactions with chain C, 13 interactions with chain F Hydrogen bonds: E:S.26, E:K.29, E:N.30, E:N.30, E:Q.48, E:R.63, E:I.64, E:R.69, B:S.26, B:K.29, B:N.30, B:N.30, B:N.30, B:Q.48, B:R.63, B:R.63, B:I.64, B:D.67, B:R.69, B:R.69, D:K.29, D:N.30, D:Q.48, D:Q.48, D:R.63, D:I.64, D:D.67, D:R.69, C:S.26, C:K.29, C:N.30, C:Q.48, C:R.63, C:R.63, C:I.64, C:D.67, C:R.69, F:S.26, F:K.29, F:N.30, F:Q.48, F:R.63, F:R.63, F:R.69 Salt bridges: E:K.29, B:K.29, D:K.29, C:K.29, F:K.29 Hydrophobic interactions: B:I.22, B:I.22, B:L.39, B:F.46, B:Q.48, B:H.70, C:D.67 Water bridges: B:N.30, B:N.30, B:N.30, B:N.30, B:N.30, B:R.63, B:R.63, B:R.63, B:R.63, B:R.63, B:R.69, B:R.69, B:R.69, B:R.69, B:R.69, F:N.30, F:N.30, F:N.30, F:N.30, F:N.30 FMN.9: 94 residues within 4Å: Chain B: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain C: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain D: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain E: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain F: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Ligands: FMN.3, FMN.5, FMN.7, FMN.11 76 PLIP interactions: 9 interactions with chain E, 34 interactions with chain B, 9 interactions with chain D, 11 interactions with chain C, 13 interactions with chain F Hydrogen bonds: E:S.26, E:K.29, E:N.30, E:N.30, E:Q.48, E:R.63, E:I.64, E:R.69, B:S.26, B:K.29, B:N.30, B:N.30, B:N.30, B:Q.48, B:R.63, B:R.63, B:I.64, B:D.67, B:R.69, B:R.69, D:K.29, D:N.30, D:Q.48, D:Q.48, D:R.63, D:I.64, D:D.67, D:R.69, C:S.26, C:K.29, C:N.30, C:Q.48, C:R.63, C:R.63, C:I.64, C:D.67, C:R.69, F:S.26, F:K.29, F:N.30, F:Q.48, F:R.63, F:R.63, F:R.69 Salt bridges: E:K.29, B:K.29, D:K.29, C:K.29, F:K.29 Hydrophobic interactions: B:I.22, B:I.22, B:L.39, B:F.46, B:Q.48, B:H.70, C:D.67 Water bridges: B:N.30, B:N.30, B:N.30, B:N.30, B:N.30, B:R.63, B:R.63, B:R.63, B:R.63, B:R.63, B:R.69, B:R.69, B:R.69, B:R.69, B:R.69, F:N.30, F:N.30, F:N.30, F:N.30, F:N.30 FMN.11: 94 residues within 4Å: Chain B: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain C: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain D: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain E: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Chain F: Y.6, S.8, I.22, I.25, S.26, K.29, N.30, L.39, F.46, Q.48, L.50, I.60, R.63, I.64, D.67, R.69, H.70, M.92 Ligands: FMN.3, FMN.5, FMN.7, FMN.9 76 PLIP interactions: 9 interactions with chain E, 34 interactions with chain B, 9 interactions with chain D, 11 interactions with chain C, 13 interactions with chain F Hydrogen bonds: E:S.26, E:K.29, E:N.30, E:N.30, E:Q.48, E:R.63, E:I.64, E:R.69, B:S.26, B:K.29, B:N.30, B:N.30, B:N.30, B:Q.48, B:R.63, B:R.63, B:I.64, B:D.67, B:R.69, B:R.69, D:K.29, D:N.30, D:Q.48, D:Q.48, D:R.63, D:I.64, D:D.67, D:R.69, C:S.26, C:K.29, C:N.30, C:Q.48, C:R.63, C:R.63, C:I.64, C:D.67, C:R.69, F:S.26, F:K.29, F:N.30, F:Q.48, F:R.63, F:R.63, F:R.69 Salt bridges: E:K.29, B:K.29, D:K.29, C:K.29, F:K.29 Hydrophobic interactions: B:I.22, B:I.22, B:L.39, B:F.46, B:Q.48, B:H.70, C:D.67 Water bridges: B:N.30, B:N.30, B:N.30, B:N.30, B:N.30, B:R.63, B:R.63, B:R.63, B:R.63, B:R.63, B:R.69, B:R.69, B:R.69, B:R.69, B:R.69, F:N.30, F:N.30, F:N.30, F:N.30, F:N.30

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.156, I.157, F.160, D.200 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.156, A:I.157, A:D.200, H2O.2, H2O.10 MG.4: 24 residues within 4Å: Chain B: D.156, I.157, F.160, D.200 Chain C: D.156, I.157, F.160, D.200 Chain D: D.156, I.157, F.160, D.200 Chain E: D.156, I.157, F.160, D.200 Chain F: D.156, I.157, F.160, D.200 Ligands: MG.6, MG.8, MG.10, MG.12 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Metal complexes: C:I.157, C:D.200, B:I.157, B:D.200 MG.6: 24 residues within 4Å: Chain B: D.156, I.157, F.160, D.200 Chain C: D.156, I.157, F.160, D.200 Chain D: D.156, I.157, F.160, D.200 Chain E: D.156, I.157, F.160, D.200 Chain F: D.156, I.157, F.160, D.200 Ligands: MG.4, MG.8, MG.10, MG.12 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Metal complexes: C:I.157, C:D.200, B:I.157, B:D.200 MG.8: 24 residues within 4Å: Chain B: D.156, I.157, F.160, D.200 Chain C: D.156, I.157, F.160, D.200 Chain D: D.156, I.157, F.160, D.200 Chain E: D.156, I.157, F.160, D.200 Chain F: D.156, I.157, F.160, D.200 Ligands: MG.4, MG.6, MG.10, MG.12 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Metal complexes: C:I.157, C:D.200, B:I.157, B:D.200 MG.10: 24 residues within 4Å: Chain B: D.156, I.157, F.160, D.200 Chain C: D.156, I.157, F.160, D.200 Chain D: D.156, I.157, F.160, D.200 Chain E: D.156, I.157, F.160, D.200 Chain F: D.156, I.157, F.160, D.200 Ligands: MG.4, MG.6, MG.8, MG.12 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Metal complexes: C:I.157, C:D.200, B:I.157, B:D.200 MG.12: 24 residues within 4Å: Chain B: D.156, I.157, F.160, D.200 Chain C: D.156, I.157, F.160, D.200 Chain D: D.156, I.157, F.160, D.200 Chain E: D.156, I.157, F.160, D.200 Chain F: D.156, I.157, F.160, D.200 Ligands: MG.4, MG.6, MG.8, MG.10 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Metal complexes: C:I.157, C:D.200, B:I.157, B:D.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chretien, A. et al., Light-induced Trp in /Met out Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC. J.Mol.Biol. (2024)

Release Date

2023-11-01

Peptides

Family 3 adenylate cyclase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Family 3 adenylate cyclase

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