SMTL ID : 4clz.1

Crystal structure of human soluble Adenylyl Cyclase with Inhibitor 4, 4'-Diisothiocyano-2,2'-stilbenedisulfonic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

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

ACT.1: 7 residues within 4Å: Chain A: K.95, L.102, L.166, V.167, V.172, F.336, M.337 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.102, A:V.167, A:V.172 Hydrogen bonds: A:V.167, A:V.167, A:M.337 Salt bridges: A:K.95 ACT.2: 4 residues within 4Å: Chain A: Y.77, H.78, A.81, F.130 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.130 Hydrogen bonds: A:L.129 Water bridges: A:A.81 Salt bridges: A:H.78 ACT.3: 4 residues within 4Å: Chain A: S.80, H.398, T.399 Chain C: Q.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.80, A:S.80 Salt bridges: A:H.398 ACT.4: 5 residues within 4Å: Chain A: N.76, G.397, H.398, T.399, H.402 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.402 Hydrogen bonds: A:T.399 Water bridges: A:N.76, A:Q.283, A:T.399 Salt bridges: A:H.402 ACT.16: 7 residues within 4Å: Chain B: K.95, L.102, L.166, V.167, V.172, F.336, M.337 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.102, B:V.167, B:V.172 Hydrogen bonds: B:V.167, B:V.167, B:M.337 Salt bridges: B:K.95 ACT.17: 4 residues within 4Å: Chain B: Y.77, H.78, A.81, F.130 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.130 Hydrogen bonds: B:L.129 Water bridges: B:A.81 Salt bridges: B:H.78 ACT.18: 4 residues within 4Å: Chain A: Q.9 Chain B: S.80, H.398, T.399 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.80, B:S.80 Salt bridges: B:H.398 ACT.19: 5 residues within 4Å: Chain B: N.76, G.397, H.398, T.399, H.402 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:H.402 Hydrogen bonds: B:T.399 Water bridges: B:N.76, B:Q.283, B:T.399 Salt bridges: B:H.402 ACT.31: 7 residues within 4Å: Chain C: K.95, L.102, L.166, V.167, V.172, F.336, M.337 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.102, C:V.167, C:V.172 Hydrogen bonds: C:V.167, C:V.167, C:M.337 Salt bridges: C:K.95 ACT.32: 4 residues within 4Å: Chain C: Y.77, H.78, A.81, F.130 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.130 Hydrogen bonds: C:L.129 Water bridges: C:A.81 Salt bridges: C:H.78 ACT.33: 4 residues within 4Å: Chain B: Q.9 Chain C: S.80, H.398, T.399 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.80, C:S.80 Salt bridges: C:H.398 ACT.34: 5 residues within 4Å: Chain C: N.76, G.397, H.398, T.399, H.402 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:H.402 Hydrogen bonds: C:T.399 Water bridges: C:N.76, C:Q.283, C:T.399 Salt bridges: C:H.402

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

EDO.5: 9 residues within 4Å: Chain A: L.87, I.88, Y.240, P.241, K.246, L.248, L.249 Chain C: N.2, P.4 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:L.87, A:K.246, C:N.2 Water bridges: A:G.90 EDO.6: 6 residues within 4Å: Chain A: T.322, L.325, K.326, G.330, Q.331, I.332 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.332 EDO.7: 2 residues within 4Å: Chain A: R.106, M.237 5 PLIP interactions: 5 interactions with chain A Water bridges: A:G.90, A:R.106, A:R.106, A:H.238, A:H.238 EDO.20: 9 residues within 4Å: Chain A: N.2, P.4 Chain B: L.87, I.88, Y.240, P.241, K.246, L.248, L.249 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.87, B:K.246, A:N.2 Water bridges: B:G.90 EDO.21: 6 residues within 4Å: Chain B: T.322, L.325, K.326, G.330, Q.331, I.332 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.332 EDO.22: 2 residues within 4Å: Chain B: R.106, M.237 5 PLIP interactions: 5 interactions with chain B Water bridges: B:G.90, B:R.106, B:R.106, B:H.238, B:H.238 EDO.35: 9 residues within 4Å: Chain B: N.2, P.4 Chain C: L.87, I.88, Y.240, P.241, K.246, L.248, L.249 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:L.87, C:K.246, B:N.2 Water bridges: C:G.90 EDO.36: 6 residues within 4Å: Chain C: T.322, L.325, K.326, G.330, Q.331, I.332 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.332 EDO.37: 2 residues within 4Å: Chain C: R.106, M.237 5 PLIP interactions: 5 interactions with chain C Water bridges: C:G.90, C:R.106, C:R.106, C:H.238, C:H.238

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 10 residues within 4Å: Chain A: A.97, G.98, F.296, N.333, K.334, F.336, L.345, T.405, V.406, V.411 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.98, A:N.333, A:N.333, A:V.406 PEG.9: 6 residues within 4Å: Chain A: Q.9, D.10, W.11, P.12, R.15, N.279 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.9, A:D.10, A:R.15, A:N.279 Water bridges: A:R.15, A:R.15, B:N.76 PEG.10: 7 residues within 4Å: Chain A: K.95, H.164, Y.268, I.332, N.333, K.334, V.335 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.95, A:K.95, A:Y.268, A:V.335 Water bridges: A:M.270 PEG.23: 10 residues within 4Å: Chain B: A.97, G.98, F.296, N.333, K.334, F.336, L.345, T.405, V.406, V.411 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.98, B:N.333, B:N.333, B:V.406 PEG.24: 6 residues within 4Å: Chain B: Q.9, D.10, W.11, P.12, R.15, N.279 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.9, B:D.10, B:R.15, B:N.279 Water bridges: B:R.15, B:R.15, C:N.76 PEG.25: 7 residues within 4Å: Chain B: K.95, H.164, Y.268, I.332, N.333, K.334, V.335 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.95, B:K.95, B:Y.268, B:V.335 Water bridges: B:M.270 PEG.38: 10 residues within 4Å: Chain C: A.97, G.98, F.296, N.333, K.334, F.336, L.345, T.405, V.406, V.411 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.98, C:N.333, C:N.333, C:V.406 PEG.39: 6 residues within 4Å: Chain C: Q.9, D.10, W.11, P.12, R.15, N.279 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.9, C:D.10, C:R.15, C:N.279 Water bridges: C:R.15, C:R.15, A:N.76 PEG.40: 7 residues within 4Å: Chain C: K.95, H.164, Y.268, I.332, N.333, K.334, V.335 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.95, C:K.95, C:Y.268, C:V.335 Water bridges: C:M.270

9 x 4DS: 4,4'-Diisothiocyano-2,2'-stilbenedisulfonic acid(Non-covalent)

4DS.11: 15 residues within 4Å: Chain A: F.8, D.10, V.14, R.15, A.18, R.250, A.252, C.253, Q.276, I.277, N.279, Q.281, Q.283, T.399, V.400 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.8, A:R.15, A:A.18, A:Q.283, A:T.399 Hydrogen bonds: A:Q.276 Water bridges: A:R.15, A:H.19, A:H.19, A:N.279, A:H.402 Salt bridges: A:R.15 pi-Cation interactions: A:R.15 4DS.12: 16 residues within 4Å: Chain A: F.45, K.95, F.96, A.97, A.100, L.101, L.102, R.176, N.180, F.336, M.337, F.338, D.339, R.416, M.419, Y.420 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.45, A:A.97, A:F.336, A:F.338, A:F.338, A:F.338 Hydrogen bonds: A:R.176, A:N.180, A:D.339, A:D.339, A:R.416 Water bridges: A:K.340 Salt bridges: A:R.176 pi-Cation interactions: A:R.176 4DS.13: 11 residues within 4Å: Chain A: F.51, M.54, K.57, F.58, M.62, Y.63, I.74, H.78 Chain C: P.259, E.260, M.263 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.58, A:I.74, C:P.259, C:E.260 4DS.26: 15 residues within 4Å: Chain B: F.8, D.10, V.14, R.15, A.18, R.250, A.252, C.253, Q.276, I.277, N.279, Q.281, Q.283, T.399, V.400 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.8, B:R.15, B:A.18, B:Q.283, B:T.399 Hydrogen bonds: B:Q.276 Water bridges: B:R.15, B:H.19, B:H.19, B:N.279, B:H.402 Salt bridges: B:R.15 pi-Cation interactions: B:R.15 4DS.27: 16 residues within 4Å: Chain B: F.45, K.95, F.96, A.97, A.100, L.101, L.102, R.176, N.180, F.336, M.337, F.338, D.339, R.416, M.419, Y.420 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.45, B:A.97, B:F.336, B:F.338, B:F.338, B:F.338 Hydrogen bonds: B:R.176, B:N.180, B:D.339, B:D.339, B:R.416 Water bridges: B:K.340 Salt bridges: B:R.176 pi-Cation interactions: B:R.176 4DS.28: 11 residues within 4Å: Chain A: P.259, E.260, M.263 Chain B: F.51, M.54, K.57, F.58, M.62, Y.63, I.74, H.78 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.58, B:I.74, A:P.259, A:E.260 4DS.41: 15 residues within 4Å: Chain C: F.8, D.10, V.14, R.15, A.18, R.250, A.252, C.253, Q.276, I.277, N.279, Q.281, Q.283, T.399, V.400 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.8, C:R.15, C:A.18, C:Q.283, C:T.399 Hydrogen bonds: C:Q.276 Water bridges: C:R.15, C:H.19, C:H.19, C:N.279, C:H.402 Salt bridges: C:R.15 pi-Cation interactions: C:R.15 4DS.42: 16 residues within 4Å: Chain C: F.45, K.95, F.96, A.97, A.100, L.101, L.102, R.176, N.180, F.336, M.337, F.338, D.339, R.416, M.419, Y.420 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.45, C:A.97, C:F.336, C:F.338, C:F.338, C:F.338 Hydrogen bonds: C:R.176, C:N.180, C:D.339, C:D.339, C:R.416 Water bridges: C:K.340 Salt bridges: C:R.176 pi-Cation interactions: C:R.176 4DS.43: 11 residues within 4Å: Chain B: P.259, E.260, M.263 Chain C: F.51, M.54, K.57, F.58, M.62, Y.63, I.74, H.78 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:P.259, B:E.260, C:F.58, C:I.74

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.14: 8 residues within 4Å: Chain A: I.24, V.25, G.27, H.28, F.29, L.261, S.264, Y.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.264, A:Y.268 pi-Cation interactions: A:F.29 DMS.15: 2 residues within 4Å: Chain A: Q.111, N.114 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.111 DMS.29: 8 residues within 4Å: Chain B: I.24, V.25, G.27, H.28, F.29, L.261, S.264, Y.268 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.264, B:Y.268 pi-Cation interactions: B:F.29 DMS.30: 2 residues within 4Å: Chain B: Q.111, N.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.111 DMS.44: 8 residues within 4Å: Chain C: I.24, V.25, G.27, H.28, F.29, L.261, S.264, Y.268 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.264, C:Y.268 pi-Cation interactions: C:F.29 DMS.45: 2 residues within 4Å: Chain C: Q.111, N.114 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.111

Links

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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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