SMTL ID : 4clk.1

Crystal structure of human soluble Adenylyl Cyclase in complex with alpha,beta-methyleneadenosine-5'-triphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

3 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.1: 22 residues within 4Å: Chain A: D.47, I.48, S.49, G.50, F.51, T.52, A.97, G.98, D.99, K.144, R.176, F.296, F.336, F.338, L.345, T.405, V.406, V.411, N.412, A.415, R.416 Ligands: CA.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.49, A:G.50, A:F.51, A:T.52, A:T.52, A:T.52, A:K.144, A:R.176, A:V.406, A:N.412 Water bridges: A:A.53, A:G.98, A:G.98 APC.8: 22 residues within 4Å: Chain B: D.47, I.48, S.49, G.50, F.51, T.52, A.97, G.98, D.99, K.144, R.176, F.296, F.336, F.338, L.345, T.405, V.406, V.411, N.412, A.415, R.416 Ligands: CA.10 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.49, B:G.50, B:F.51, B:T.52, B:T.52, B:T.52, B:K.144, B:R.176, B:V.406, B:N.412 Water bridges: B:A.53, B:G.98, B:G.98 APC.15: 22 residues within 4Å: Chain C: D.47, I.48, S.49, G.50, F.51, T.52, A.97, G.98, D.99, K.144, R.176, F.296, F.336, F.338, L.345, T.405, V.406, V.411, N.412, A.415, R.416 Ligands: CA.17 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.49, C:G.50, C:F.51, C:T.52, C:T.52, C:T.52, C:K.144, C:R.176, C:V.406, C:N.412 Water bridges: C:A.53, C:G.98, C:G.98

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

CL.2: 3 residues within 4Å: Chain A: K.95, L.166, V.167 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: K.95, L.166, V.167 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain C: K.95, L.166, V.167 Ligand excluded by PLIP

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.47, I.48, D.99 Ligands: APC.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.47, A:D.99, H2O.3 CA.10: 4 residues within 4Å: Chain B: D.47, I.48, D.99 Ligands: APC.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.47, B:D.99, H2O.9 CA.17: 4 residues within 4Å: Chain C: D.47, I.48, D.99 Ligands: APC.15 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.47, C:D.99, H2O.16

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

EDO.4: 4 residues within 4Å: Chain A: H.398, T.399, V.400 Chain B: E.7 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain A: T.322, K.326, G.330, Q.331, I.332 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.322, A:I.332 Water bridges: A:T.322 EDO.11: 4 residues within 4Å: Chain B: H.398, T.399, V.400 Chain C: E.7 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain B: T.322, K.326, G.330, Q.331, I.332 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.322, B:I.332 Water bridges: B:T.322 EDO.18: 4 residues within 4Å: Chain A: E.7 Chain C: H.398, T.399, V.400 No protein-ligand interaction detected (PLIP) EDO.19: 5 residues within 4Å: Chain C: T.322, K.326, G.330, Q.331, I.332 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.322, C:I.332 Water bridges: C:T.322

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain A: I.24, V.25, Y.26, G.27, H.28, F.29, L.261, S.264, L.265 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.25, A:H.28, A:S.264, A:S.264 Water bridges: A:S.264, A:Y.268 GOL.7: 6 residues within 4Å: Chain A: Y.432, S.435, N.436, L.437, A.439, F.442 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.435, A:L.437, A:L.437 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.25, B:H.28, B:S.264, B:S.264 Water bridges: B:S.264, B:Y.268 GOL.14: 6 residues within 4Å: Chain B: Y.432, S.435, N.436, L.437, A.439, F.442 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.435, B:L.437, B:L.437 GOL.20: 9 residues within 4Å: Chain C: I.24, V.25, Y.26, G.27, H.28, F.29, L.261, S.264, L.265 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:V.25, C:H.28, C:S.264, C:S.264 Water bridges: C:S.264, C:Y.268 GOL.21: 6 residues within 4Å: Chain C: Y.432, S.435, N.436, L.437, A.439, F.442 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.435, C:L.437, C:L.437

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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