SMTL ID : 2nzm.1

Hexasaccharide I bound to Bacillus subtilis pectate lyase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

ADA-ADA-ADA-ADA-ADA.1: 21 residues within 4Å: Chain A: K.118, D.173, N.178, N.180, Q.182, N.189, D.223, D.227, S.229, N.230, K.247, I.250, S.253, K.257, Q.278, R.282, R.284, F.339 Ligands: CA.2, CA.3, CA.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.189, A:N.189, A:N.230 Water bridges: A:K.118, A:K.118, A:K.118, A:Q.146, A:Q.182, A:S.229 Salt bridges: A:K.118

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.184, D.223, D.227 Ligands: ADA-ADA-ADA-ADA-ADA.1, CA.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.184, A:D.223, A:D.227, H2O.2, H2O.19 CA.3: 4 residues within 4Å: Chain A: D.173, N.180 Ligands: ADA-ADA-ADA-ADA-ADA.1, ADA-ADA-ADA-ADA-ADA.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.173, H2O.7, H2O.7 CA.4: 4 residues within 4Å: Chain A: D.223 Ligands: ADA-ADA-ADA-ADA-ADA.1, ADA-ADA-ADA-ADA-ADA.1, CA.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.223, A:D.223, H2O.4, H2O.5, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seyedarabi, A. et al., Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase. Biochemistry (2010)

Release Date

2007-11-20

Peptides

Pectate lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pectate lyase

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