SMTL ID : 5iv3.1

Crystal structure of human soluble adenylyl cyclase in complex with alpha,beta-methyleneadenosine-5'-triphosphate and the allosteric inhibitor LRE1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

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

ACT.1: 6 residues within 4Å: Chain A: K.95, H.164, N.333, K.334, V.335 Ligands: GOL.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.335 Water bridges: A:K.95, A:F.165 Salt bridges: A:K.95, A:H.164 ACT.2: 4 residues within 4Å: Chain A: F.338, A.415 Ligands: APC.7, PEG.9 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: H.19, K.95, F.165, Y.268, K.334, E.403 Ligands: ACT.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.19, A:K.334, A:K.334 Water bridges: A:K.95, A:R.401, A:Y.404 GOL.4: 7 residues within 4Å: Chain A: P.356, D.357, E.358, L.359, T.360, G.434, N.436 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.358, A:L.359, A:T.360 Water bridges: A:P.356 GOL.5: 8 residues within 4Å: Chain A: I.24, G.27, H.28, F.29, R.33, L.261, S.264, Y.268 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:V.25, A:H.28, A:F.29, A:F.29, A:R.33, A:S.264, A:Y.268 Water bridges: A:S.163

1 x LRI: 6-chloro-N~4~-cyclopropyl-N~4~-[(thiophen-2-yl)methyl]pyrimidine-2,4-diamine(Non-covalent)

LRI.6: 13 residues within 4Å: Chain A: F.45, K.95, A.97, L.102, F.165, L.166, V.167, V.172, V.175, R.176, F.336, M.337 Ligands: APC.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.95, A:K.95, A:A.97, A:L.102, A:V.175, A:R.176, A:F.336 Hydrogen bonds: A:V.167, A:M.337, A:M.337 pi-Stacking: A:F.45

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

APC.7: 19 residues within 4Å: Chain A: F.45, D.47, I.48, S.49, G.50, F.51, T.52, A.97, D.99, R.176, Q.179, N.180, F.338, N.412, R.416 Ligands: ACT.2, LRI.6, CA.8, PEG.9 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.49, A:G.50, A:T.52, A:D.99, A:R.176, A:Q.179, A:Q.179, A:N.412, A:R.416 Water bridges: A:A.53, A:D.99

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain A: D.47, I.48, D.99 Ligands: APC.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.47, A:I.48, A:D.99, H2O.8

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

PEG.9: 10 residues within 4Å: Chain A: A.97, G.98, F.336, L.345, T.405, V.406, V.411, N.412 Ligands: ACT.2, APC.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.406, A:N.412 Water bridges: A:T.405

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

EDO.10: 5 residues within 4Å: Chain A: T.322, L.325, G.330, Q.331, I.332 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.332

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

CL.11: 3 residues within 4Å: Chain A: S.80, H.398, T.399 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramos-Espiritu, L. et al., Discovery of LRE1 as a specific and allosteric inhibitor of soluble adenylyl cyclase. Nat.Chem.Biol. (2016)

Release Date

2016-08-17

Peptides

Adenylate cyclase type 10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenylate cyclase type 10

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