SMTL ID : 5gz4.1

Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

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.1: 4 residues within 4Å: Chain A: L.639, A.640, I.641, N.723 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.2: 9 residues within 4Å: Chain A: T.177, H.405, P.487, N.488, N.489, D.709, G.710, H.711, L.798 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.709, A:D.709

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: D.282, H.286, H.439 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.282, A:D.282, A:H.286, A:H.439, H2O.1 ZN.4: 4 residues within 4Å: Chain A: D.124, T.162, D.329, H.330 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.5: 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 EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain A: L.137, P.139, Q.300, D.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.300, A:D.303, A:D.303

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

NAG.7: 4 residues within 4Å: Chain A: G.209, Q.210, Y.218, N.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.210, A:Y.218, A:N.236 NAG.8: 1 residues within 4Å: Chain A: N.247 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain A: N.191, N.193, R.363 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.193, A:N.193 Water bridges: A:K.365, A:V.367 NAG.10: 4 residues within 4Å: Chain A: N.16, K.31, Q.43, V.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.16

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). 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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