SMTL ID : 7cba.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

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

NAG-NAG-BMA.1: 10 residues within 4Å: Chain A: L.173, E.176, T.177, H.405, P.487, N.488, N.489, D.709, H.711, L.798 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: N.191, N.193, F.353, R.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.193, A:R.363, A:K.365 NAG.3: 3 residues within 4Å: Chain A: N.247, T.250, P.251 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: N.742, T.744, K.745 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.742, A:K.745 NAG.5: 3 residues within 4Å: Chain A: Q.210, Y.218, N.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.210

2 x ZN: ZINC ION(Non-covalent)

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

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain A: D.705, N.707, D.709, H.711, F.712, D.713 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.705, A:D.709, A:H.711, A:D.713

1 x IRH: isorhamnetin(Non-covalent)

IRH.9: 14 residues within 4Å: Chain A: D.124, F.163, M.201, F.227, W.228, P.229, E.232, Y.246, K.248, Y.277, E.279, D.282, T.283 Ligands: CIT.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.246, A:E.279 Hydrogen bonds: A:K.248, A:D.282, A:T.283 pi-Stacking: A:F.163, A:Y.246, A:Y.246

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.10: 11 residues within 4Å: Chain A: D.124, K.161, T.162, N.183, D.282, H.286, H.330, H.439 Ligands: ZN.6, ZN.7, IRH.9 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.162, A:N.183, A:D.282 Salt bridges: A:H.286, A:H.330, A:H.439, A:H.439

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, I.J. et al., Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra) in complex with isorhamnetin and citrate. To Be Published

Release Date

2021-07-21

Peptides

Venom phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Venom phosphodiesterase

Related Entries With Identical Sequence