SMTL ID : 5h7w.1

Crystal structure of 5'-nucleotidase from venom of Naja atra

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 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: 7 residues within 4Å: Chain A: Y.320, N.322, T.324, H.326, A.327, H.331 Chain B: R.456 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.326 NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: R.456 Chain B: Y.320, N.322, T.324, H.326, A.327, H.331 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.326

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

NAG.3: 2 residues within 4Å: Chain A: N.308, Q.312 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.308 Water bridges: A:N.308, A:N.308

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.12, H.14, D.60 Ligands: ZN.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.12, A:D.60, H2O.1, H2O.2, H2O.6 ZN.5: 6 residues within 4Å: Chain A: D.12, D.60, N.92, H.195, H.218 Ligands: ZN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.60, A:H.195, A:H.218, H2O.6 ZN.7: 4 residues within 4Å: Chain B: D.12, H.14, D.60 Ligands: ZN.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.12, B:H.14, B:D.60, H2O.22, H2O.23 ZN.8: 6 residues within 4Å: Chain B: D.12, D.60, N.92, H.195, H.218 Ligands: ZN.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.60, B:H.195, B:H.218, H2O.23

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 3 residues within 4Å: Chain A: N.188, D.212, G.273 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.188, A:D.212, A:G.273, H2O.2, H2O.8 CA.9: 3 residues within 4Å: Chain B: N.188, D.212, G.273 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.188, B:D.212, B:G.273, H2O.22, H2O.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, C. et al., Crystal strucuture of Taiwan cobra (Naja atra) venom 5'-nucleotidase at 1.9 Angstroms resolution. To Be Published

Release Date

2017-11-22

Peptides

venom 5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

venom 5'-nucleotidase