SMTL ID : 2zuy.1

Crystal structure of exotype rhamnogalacturonan lyase YesX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

9 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: H.330, H.366, D.368, E.389 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.330, A:H.366, A:D.368, A:E.389, H2O.6, H2O.6 CA.2: 5 residues within 4Å: Chain A: D.472, D.474, V.476, E.478, K.495 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.472, A:D.474, A:D.474, A:V.476, A:E.478 CA.3: 6 residues within 4Å: Chain A: D.125, D.127, D.129, E.131, E.133, K.161 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.125, A:D.127, A:D.129, A:E.131, A:E.133 CA.4: 5 residues within 4Å: Chain A: D.189, D.191, D.193, K.195, E.197 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.189, A:D.191, A:D.193, A:K.195, A:E.197 CA.5: 5 residues within 4Å: Chain A: D.374, D.376, R.379, G.381, E.383 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.376, A:R.379, A:G.381, A:E.383, A:E.383 CA.6: 4 residues within 4Å: Chain A: D.120, N.576, A.578, N.580 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.120, A:N.576, A:A.578, H2O.2, H2O.7 CA.7: 6 residues within 4Å: Chain A: D.338, D.340, E.344, D.353, H.354 Ligands: CA.8 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.338, A:D.340, A:E.344, A:D.353, A:H.354, H2O.7 CA.8: 7 residues within 4Å: Chain A: D.336, V.337, D.338, D.340, K.342, E.344 Ligands: CA.7 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.336, A:D.338, A:D.340, A:K.342, A:E.344 CA.9: 6 residues within 4Å: Chain A: N.527, F.529, G.530, D.531, R.533, E.535 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.529, A:D.531, A:R.533, A:E.535, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ochiai, A. et al., Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases. J.Biol.Chem. (2009)

Release Date

2009-02-03

Peptides

YesX protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

YesX protein