SMTL ID : 8qfg.1

Cryogenic crystal structure of the Photoactivated Adenylate Cyclase OaPAC after 5 seconds of blue light illumination

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

3 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 17 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.22, A:L.39, A:L.39, A:F.46 Hydrogen bonds: A:N.30, A:N.30, A:Q.48, A:R.63, A:R.63, A:D.67, A:R.69 Salt bridges: A:K.29 FMN.5: 35 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 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 Ligands: FMN.9 23 PLIP interactions: 14 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:I.22, B:L.39, B:L.39, B:F.46 Hydrogen bonds: B:S.26, B:N.30, B:N.30, B:Q.48, B:R.63, B:R.63, B:D.67, B:R.69, B:R.69, C:S.26, C:N.30, C:Q.48, C:R.63, C:R.63, C:I.64, C:D.67, C:R.69 Salt bridges: B:K.29, C:K.29 FMN.9: 35 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 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 Ligands: FMN.5 23 PLIP interactions: 14 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:I.22, B:L.39, B:L.39, B:F.46 Hydrogen bonds: B:S.26, B:N.30, B:N.30, B:Q.48, B:R.63, B:R.63, B:D.67, B:R.69, B:R.69, C:S.26, C:N.30, C:Q.48, C:R.63, C:R.63, C:I.64, C:D.67, C:R.69 Salt bridges: B:K.29, C:K.29

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 30 residues within 4Å: Chain A: D.156, I.157, V.158, S.159, F.160, S.161, I.198, G.199, D.200, R.283 Chain B: F.154, I.198, I.267, L.268, G.269, D.270, V.272, N.273, A.276 Chain C: F.154, I.198, I.267, L.268, G.269, D.270, V.272, N.273, A.276 Ligands: MG.3, MG.4 23 PLIP interactions: 10 interactions with chain A, 4 interactions with chain C, 9 interactions with chain B Hydrogen bonds: A:I.157, A:S.159, A:F.160, A:S.161, A:D.200, C:G.269, C:D.270, C:N.273, B:G.269, B:G.269, B:D.270, B:N.273 Water bridges: A:D.156, A:D.156, A:S.161, A:S.161, C:I.267, B:I.267, B:N.273, B:N.273, B:N.273, B:N.273 Salt bridges: A:R.283 ATP.6: 34 residues within 4Å: Chain A: F.154, I.198, I.267, L.268, G.269, D.270, V.272, N.273, A.276 Chain B: D.156, I.157, V.158, S.159, F.160, S.161, I.198, G.199, D.200, R.283 Chain C: D.156, I.157, V.158, S.159, F.160, S.161, I.198, G.199, D.200, R.283 Ligands: MG.7, MG.8, ATP.10, MG.11, MG.12 31 PLIP interactions: 17 interactions with chain B, 12 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:D.156, B:D.156, B:I.157, B:S.159, B:S.159, B:F.160, B:S.161, B:S.161, C:S.159, C:F.160, C:S.161, C:S.161, C:D.200, A:G.269, A:N.273 Water bridges: B:D.156, B:D.156, B:D.156, B:D.156, B:G.199, B:G.199, B:G.199, B:G.199, C:S.159, C:S.159, C:I.198, C:I.198, C:R.283, C:R.283 Salt bridges: B:R.283, C:R.283 ATP.10: 34 residues within 4Å: Chain A: F.154, I.198, I.267, L.268, G.269, D.270, V.272, N.273, A.276 Chain B: D.156, I.157, V.158, S.159, F.160, S.161, I.198, G.199, D.200, R.283 Chain C: D.156, I.157, V.158, S.159, F.160, S.161, I.198, G.199, D.200, R.283 Ligands: ATP.6, MG.7, MG.8, MG.11, MG.12 31 PLIP interactions: 17 interactions with chain B, 12 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:D.156, B:D.156, B:I.157, B:S.159, B:S.159, B:F.160, B:S.161, B:S.161, C:S.159, C:F.160, C:S.161, C:S.161, C:D.200, A:G.269, A:N.273 Water bridges: B:D.156, B:D.156, B:D.156, B:D.156, B:G.199, B:G.199, B:G.199, B:G.199, C:S.159, C:S.159, C:I.198, C:I.198, C:R.283, C:R.283 Salt bridges: B:R.283, C:R.283

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: D.156, I.157, F.160, D.200, R.283 Ligands: ATP.2, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.156, A:I.157, A:D.200 MG.4: 5 residues within 4Å: Chain A: D.156, D.200, C.201 Ligands: ATP.2, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.156, A:D.200, H2O.2, H2O.3 MG.7: 15 residues within 4Å: Chain B: D.156, I.157, F.160, D.200, R.283 Chain C: D.156, I.157, F.160, D.200, R.283 Ligands: ATP.6, MG.8, ATP.10, MG.11, MG.12 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Metal complexes: B:D.156, B:I.157, B:D.200, C:D.156, C:D.200 MG.8: 11 residues within 4Å: Chain B: D.156, D.200, C.201 Chain C: D.156, D.200, C.201 Ligands: ATP.6, MG.7, ATP.10, MG.11, MG.12 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:D.156, B:D.200, C:D.200, H2O.7, H2O.11 MG.11: 15 residues within 4Å: Chain B: D.156, I.157, F.160, D.200, R.283 Chain C: D.156, I.157, F.160, D.200, R.283 Ligands: ATP.6, MG.7, MG.8, ATP.10, MG.12 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Metal complexes: B:D.156, B:I.157, B:D.200, C:D.156, C:D.200 MG.12: 11 residues within 4Å: Chain B: D.156, D.200, C.201 Chain C: D.156, D.200, C.201 Ligands: ATP.6, MG.7, MG.8, ATP.10, MG.11 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:D.156, B:D.200, C:D.200, H2O.7, H2O.11

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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Family 3 adenylate cyclase

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