SMTL ID : 2z8s.2 (1 other biounit)

Crystal structure of rhamnogalacturonan lyase YesW complexed with digalacturonic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x ADA- ADA: alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid(Non-covalent)

ADA-ADA.1: 8 residues within 4Å: Chain A: D.141, Q.144, H.326, D.364, R.415, T.497, K.498, Y.558 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.498 Water bridges: A:D.364, A:E.385, A:G.414, A:K.498 Salt bridges: A:R.415, A:K.498

10 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: H.326, H.362, D.364, E.385 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.326, A:H.362, A:D.364, A:E.385, H2O.5, H2O.5 CA.3: 5 residues within 4Å: Chain A: D.116, N.555, I.556, A.557, N.559 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.116, A:N.555, A:A.557, H2O.1, H2O.5 CA.4: 4 residues within 4Å: Chain A: D.459, D.461, L.463, E.465 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.459, A:D.461, A:D.461, A:L.463, A:E.465 CA.5: 6 residues within 4Å: Chain A: D.420, D.422, Y.425, P.426, G.427, E.429 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.422, A:Y.425, A:G.427, A:E.429, H2O.6 CA.6: 6 residues within 4Å: Chain A: D.332, V.333, D.334, D.336, K.338, E.340 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.332, A:D.334, A:D.336, A:E.340, A:E.340 CA.7: 6 residues within 4Å: Chain A: D.370, D.372, R.375, P.376, G.377, E.379 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.370, A:D.372, A:G.377, A:E.379, A:E.379 CA.8: 6 residues within 4Å: Chain A: D.506, L.508, G.509, D.510, R.512, E.514 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.506, A:L.508, A:D.510, A:R.512, A:E.514 CA.9: 6 residues within 4Å: Chain A: D.185, D.187, G.188, D.189, K.191, E.193 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.185, A:D.187, A:D.189, A:K.191, A:E.193 CA.10: 7 residues within 4Å: Chain A: D.121, V.122, D.123, D.125, Q.127, E.129, K.157 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.121, A:D.123, A:D.125, A:Q.127, A:E.129 CA.11: 5 residues within 4Å: Chain A: D.334, D.336, E.340, D.349, H.350 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.334, A:D.336, A:E.340, A:D.349, A:H.350

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ochiai, A. et al., A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER. J.Biol.Chem. (2007)

Release Date

2007-10-16

Peptides

YesW protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

YesW protein

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