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

Pectate lyase B from Verticillium dahliae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.122, D.151, G.152, D.155 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.122, A:D.122, A:D.151, H2O.3, H2O.13

6 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.2: 6 residues within 4Å: Chain A: T.44, T.46, V.66, K.68, Q.88 Ligands: MAN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.88 MAN.3: 8 residues within 4Å: Chain A: V.21, T.22, G.42, A.43, T.44, N.64 Ligands: MAN.2, MAN.6 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.42, A:N.64, A:N.64 MAN.4: 6 residues within 4Å: Chain A: T.46, V.47, S.48, T.49, Q.52, K.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.52, A:K.68 MAN.5: 6 residues within 4Å: Chain A: L.50, A.51, T.54, K.55, E.58, A.75 6 PLIP interactions: 6 interactions with chain A Water bridges: A:A.51, A:A.51, A:T.54, A:E.58, A:E.58, A:E.58 MAN.6: 5 residues within 4Å: Chain A: S.20, T.22, K.40, G.41 Ligands: MAN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.41 MAN.7: 7 residues within 4Å: Chain A: T.45, T.46, V.47, Q.52, K.55, A.56, L.63 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.52 Water bridges: A:Q.52, A:Q.52, A:Q.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Safran, J. et al., The specificity of pectate lyase VdPelB from Verticilium dahliae is highlighted by structural, dynamical and biochemical characterizations. Int.J.Biol.Macromol. (2023)

Release Date

2022-07-13

Peptides

Pectate lyase B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pectate lyase B

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