SMTL ID : 5gz5.1

Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra) in complex with AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 9 residues within 4Å: Chain A: L.173, T.177, H.405, P.487, N.488, N.489, D.709, H.711, L.798 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 3 residues within 4Å: Chain A: L.639, A.640, N.723 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.3: 3 residues within 4Å: Chain A: N.742, T.744, K.745 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.742, A:T.744 Hydrophobic interactions: A:K.745

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 4 residues within 4Å: Chain A: N.191, N.193, F.353, R.363 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.191, A:N.193, A:R.363 Water bridges: A:R.363, A:V.367 NAG.5: 4 residues within 4Å: Chain A: G.209, Q.210, Y.218, N.236 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.218, A:N.236 NAG.6: 3 residues within 4Å: Chain A: N.247, S.249, P.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.247

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: D.282, H.286, H.439 Ligands: AMP.10 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.282, A:D.282, A:H.286, A:H.439, AMP.10 ZN.8: 6 residues within 4Å: Chain A: D.124, T.162, D.282, D.329, H.330 Ligands: AMP.10 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.124, A:D.124, A:T.162, A:D.329, A:H.330

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 5 residues within 4Å: Chain A: D.705, N.707, D.709, H.711, D.713 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.705, A:D.709, A:H.711, A:D.713, A:D.713

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.10: 16 residues within 4Å: Chain A: T.162, F.163, N.183, L.196, W.228, P.229, E.232, Y.246, K.248, Y.277, D.282, H.286, H.330, H.439 Ligands: ZN.7, ZN.8 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.162, A:N.183, A:W.228, A:W.228, A:E.232, A:K.248 Water bridges: A:K.248, A:K.248, A:H.439 Salt bridges: A:H.286, A:H.439 pi-Stacking: A:F.163, A:F.163, A:Y.246, A:Y.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, C.C. et al., Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra) in complex with AMP. To Be Published

Release Date

2017-09-27

Peptides

Snake venom phosphodiesterase (PDE): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Snake venom phosphodiesterase (PDE)

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