SMTL ID : 7d0v.1

Crystal structure of Taiwan cobra 5'-nucleotidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

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

NAG-FUC.1: 4 residues within 4Å: Chain A: Y.70, N.308, Y.309, Q.312 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.309 Hydrogen bonds: A:N.308 Water bridges: A:N.308, A:N.308

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.2: 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.3: 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

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.4, H2O.5 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.5 ZN.8: 5 residues within 4Å: Chain B: D.12, H.14, D.60, H.195 Ligands: ZN.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.12, B:H.14, B:D.60, H2O.11, H2O.16 ZN.9: 6 residues within 4Å: Chain B: D.12, D.60, N.92, H.195, H.218 Ligands: ZN.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.60, B:H.195, B:H.218, H2O.16

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.3, H2O.5 CA.10: 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.13, H2O.17

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

NAG.7: 4 residues within 4Å: Chain B: Y.70, N.308, Q.312, K.509 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.70, B:N.308, B:K.509, B:K.509

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsai, M.-H. et al., Crystal structure of Taiwan cobra 5'-nucleotidase. To Be Published

Release Date

2021-09-15

Peptides

Snake venom 5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Snake venom 5'-nucleotidase