SMTL ID : 4usv.1

Crystal structure of human soluble Adenylyl Cyclase with pyrophosphate resulting from soaking with ATP and Calcium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: K.95, L.166, V.167 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: K.95, L.166, V.167 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: K.95, L.166, V.167 Ligand excluded by PLIP

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: D.47, D.99 Ligands: POP.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.47, A:D.99, H2O.2, H2O.3 CA.9: 3 residues within 4Å: Chain B: D.47, D.99 Ligands: POP.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.47, B:D.99, H2O.9, H2O.10 CA.16: 3 residues within 4Å: Chain C: D.47, D.99 Ligands: POP.20 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.47, C:D.99, H2O.16, H2O.17

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

EDO.3: 7 residues within 4Å: Chain A: Y.285, L.286, E.288, R.290, P.351, C.393, Y.404 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.286, A:R.290 EDO.4: 3 residues within 4Å: Chain A: H.238, Y.239, L.251 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.240 EDO.10: 7 residues within 4Å: Chain B: Y.285, L.286, E.288, R.290, P.351, C.393, Y.404 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.286, B:R.290 EDO.11: 3 residues within 4Å: Chain B: H.238, Y.239, L.251 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.240 EDO.17: 7 residues within 4Å: Chain C: Y.285, L.286, E.288, R.290, P.351, C.393, Y.404 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.286, C:R.290 EDO.18: 3 residues within 4Å: Chain C: H.238, Y.239, L.251 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Y.240

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

ACT.5: 5 residues within 4Å: Chain A: K.95, H.164, F.165, K.334, V.335 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.95, A:K.334 Hydrogen bonds: A:F.165, A:F.165, A:V.335 Water bridges: A:H.164 Salt bridges: A:K.95, A:H.164 ACT.12: 5 residues within 4Å: Chain B: K.95, H.164, F.165, K.334, V.335 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:K.95, B:K.334 Hydrogen bonds: B:F.165, B:F.165, B:V.335 Water bridges: B:H.164 Salt bridges: B:K.95, B:H.164 ACT.19: 5 residues within 4Å: Chain C: K.95, H.164, F.165, K.334, V.335 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:K.95, C:K.334 Hydrogen bonds: C:F.165, C:F.165, C:V.335 Water bridges: C:H.164 Salt bridges: C:K.95, C:H.164

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

POP.6: 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: CA.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.47, A:G.50, A:F.51, A:T.52, A:T.52, A:N.412 Water bridges: A:G.50 Salt bridges: A:K.144 POP.13: 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: CA.9 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.47, B:G.50, B:F.51, B:T.52, B:T.52, B:N.412 Water bridges: B:G.50 Salt bridges: B:K.144 POP.20: 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: CA.16 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.47, C:G.50, C:F.51, C:T.52, C:T.52, C:N.412 Water bridges: C:G.50 Salt bridges: C:K.144

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: F.29, S.30, P.31, R.33, S.264 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.33, A:R.33 Water bridges: A:S.264, A:K.267, A:K.267 GOL.14: 5 residues within 4Å: Chain B: F.29, S.30, P.31, R.33, S.264 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.33, B:R.33 Water bridges: B:S.264, B:K.267, B:K.267 GOL.21: 5 residues within 4Å: Chain C: F.29, S.30, P.31, R.33, S.264 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.33, C:R.33 Water bridges: C:S.264, C:K.267, C:K.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kleinbolting, S. et al., Structural Analysis of Human Soluble Adenylyl Cyclase and Crystal Structures of its Nucleotide Complexes -Implications for Cyclase Catalysis and Evolution. FEBS J. (2014)

Release Date

2014-07-30

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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