SMTL ID : 3zwn.1

Crystal structure of Aplysia cyclase complexed with substrate NGD and product cGDPR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x CGR: CYCLIC GUANOSINE DIPHOSPHATE-RIBOSE(Non-covalent)

CGR.1: 14 residues within 4Å: Chain A: F.78, W.79, S.80, G.81, L.99, E.100, N.109, W.142, S.146, R.172, S.175, F.176, F.177, E.181 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:W.79, A:W.79, A:G.81, A:E.100, A:S.146, A:R.172, A:S.175, A:F.176, A:F.177 Water bridges: A:L.99, A:N.109, A:W.142 pi-Stacking: A:W.142, A:W.142 pi-Cation interactions: A:W.142

1 x NGD: 3-(AMINOCARBONYL)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYD ROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- YL]PYRIDINIUM(Non-covalent)

NGD.2: 17 residues within 4Å: Chain B: F.78, W.79, S.80, G.81, L.99, E.100, N.109, F.130, R.138, E.139, W.142, S.146, R.172, S.175, F.176, F.177, E.181 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.142, B:W.142, B:W.142, B:F.176 Hydrogen bonds: B:W.79, B:W.79, B:G.81, B:E.100, B:E.100, B:S.146, B:R.172, B:F.176, B:F.177 Water bridges: B:W.79, B:G.81, B:L.99, B:R.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kotaka, M. et al., Structural Studies of Intermediates Along the Cyclization Pathway of Aplysia Adp-Ribosyl Cyclase. J.Mol.Biol. (2012)

Release Date

2011-11-30

Peptides

ADP-RIBOSYL CYCLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADP-RIBOSYL CYCLASE

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