SMTL ID : 4clu.1

Crystal structure of human soluble Adenylyl Cyclase with pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: K.95, L.166, V.167 Ligands: ACT.10 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: K.95, K.334, V.335 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: K.95, L.166, V.167 Ligands: ACT.20 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: K.95, K.334, V.335 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain C: K.95, L.166, V.167 Ligands: ACT.30 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain C: K.95, K.334, V.335 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: I.24, V.25, Y.26, G.27, H.28, F.29, L.261, S.264, L.265 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.25, A:H.28, A:F.29, A:S.264, A:S.264 Water bridges: A:S.264, A:Y.268 GOL.13: 9 residues within 4Å: Chain B: I.24, V.25, Y.26, G.27, H.28, F.29, L.261, S.264, L.265 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:V.25, B:H.28, B:F.29, B:S.264, B:S.264 Water bridges: B:S.264, B:Y.268 GOL.23: 9 residues within 4Å: Chain C: I.24, V.25, Y.26, G.27, H.28, F.29, L.261, S.264, L.265 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:V.25, C:H.28, C:F.29, C:S.264, C:S.264 Water bridges: C:S.264, C:Y.268

3 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 10 residues within 4Å: Chain A: D.47, I.48, S.49, G.50, F.51, T.52, D.99, K.144, N.412 Ligands: MG.9 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.50, A:F.51, A:T.52, A:T.52, A:N.412 Water bridges: A:T.52, A:A.53, A:D.99 Salt bridges: A:K.144 POP.14: 10 residues within 4Å: Chain B: D.47, I.48, S.49, G.50, F.51, T.52, D.99, K.144, N.412 Ligands: MG.19 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.50, B:F.51, B:T.52, B:T.52, B:N.412 Water bridges: B:T.52, B:A.53, B:D.99 Salt bridges: B:K.144 POP.24: 10 residues within 4Å: Chain C: D.47, I.48, S.49, G.50, F.51, T.52, D.99, K.144, N.412 Ligands: MG.29 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.50, C:F.51, C:T.52, C:T.52, C:N.412 Water bridges: C:T.52, C:A.53, C:D.99 Salt bridges: C:K.144

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

EDO.5: 4 residues within 4Å: Chain A: T.322, L.325, Q.331, I.332 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.322, A:T.322, A:I.332 EDO.6: 5 residues within 4Å: Chain A: F.29, P.31, R.33, S.264, K.267 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.29, A:S.264, A:K.267, A:K.267 Water bridges: A:R.33, A:S.163 EDO.7: 7 residues within 4Å: Chain A: F.58, S.59, Y.63, D.65, R.66, G.67, L.289 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.65, A:G.67 Water bridges: A:S.59, A:S.60 EDO.8: 5 residues within 4Å: Chain A: V.355, P.356, D.357, E.358, L.359 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.355, A:D.357, A:E.358, A:L.359 Water bridges: A:D.357, A:T.360 EDO.15: 4 residues within 4Å: Chain B: T.322, L.325, Q.331, I.332 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.322, B:T.322, B:I.332 EDO.16: 5 residues within 4Å: Chain B: F.29, P.31, R.33, S.264, K.267 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.29, B:S.264, B:K.267, B:K.267 Water bridges: B:R.33, B:S.163 EDO.17: 7 residues within 4Å: Chain B: F.58, S.59, Y.63, D.65, R.66, G.67, L.289 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.65, B:G.67 Water bridges: B:S.59, B:S.60 EDO.18: 5 residues within 4Å: Chain B: V.355, P.356, D.357, E.358, L.359 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.355, B:D.357, B:E.358, B:L.359 Water bridges: B:D.357, B:T.360 EDO.25: 4 residues within 4Å: Chain C: T.322, L.325, Q.331, I.332 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.322, C:T.322, C:I.332 EDO.26: 5 residues within 4Å: Chain C: F.29, P.31, R.33, S.264, K.267 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:F.29, C:S.264, C:K.267, C:K.267 Water bridges: C:R.33, C:S.163 EDO.27: 7 residues within 4Å: Chain C: F.58, S.59, Y.63, D.65, R.66, G.67, L.289 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.65, C:G.67 Water bridges: C:S.59, C:S.60 EDO.28: 5 residues within 4Å: Chain C: V.355, P.356, D.357, E.358, L.359 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:V.355, C:D.357, C:E.358, C:L.359 Water bridges: C:D.357, C:T.360

3 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain A: D.47, D.99 Ligands: POP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.47, A:D.99 MG.19: 3 residues within 4Å: Chain B: D.47, D.99 Ligands: POP.14 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.47, B:D.99 MG.29: 3 residues within 4Å: Chain C: D.47, D.99 Ligands: POP.24 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.47, C:D.99

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 6 residues within 4Å: Chain A: F.45, K.95, L.102, R.176, F.336 Ligands: CL.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.102, A:F.336 Hydrogen bonds: A:K.95 Salt bridges: A:R.176 ACT.20: 6 residues within 4Å: Chain B: F.45, K.95, L.102, R.176, F.336 Ligands: CL.11 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.102, B:F.336 Hydrogen bonds: B:K.95 Salt bridges: B:R.176 ACT.30: 6 residues within 4Å: Chain C: F.45, K.95, L.102, R.176, F.336 Ligands: CL.21 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.102, C:F.336 Hydrogen bonds: C:K.95 Salt bridges: C:R.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kleinboelting, S. et al., Crystal Structures of Human Soluble Adenylyl Cyclase Reveal Mechanisms of Catalysis and of its Activation Through Bicarbonate. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-03-05

Peptides

ADENYLATE CYCLASE TYPE 10: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

ADENYLATE CYCLASE TYPE 10

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