SMTL ID : 1ofl.1

CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFATE HEXASACCHARIDE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x MAN- GCU- XYP- MXZ- GLA- BGC- RAM: alpha-D-galactopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]2-O-methyl-alpha-L-fucopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose

MAN-GCU-XYP-MXZ-GLA-BGC-RAM.1: 10 residues within 4Å: Chain A: R.174, H.177, D.208, S.209, Y.232, G.233, N.255, F.257, G.437, K.438 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.174, A:D.208, A:D.208, A:Y.232, A:E.444, A:K.438, A:K.438 Water bridges: A:R.174, A:T.436, A:K.438, A:L.440, A:E.444, A:E.444 Salt bridges: A:H.177

3 x ASG- GCD: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose(Non-covalent)

ASG-GCD.2: 10 residues within 4Å: Chain A: E.220, R.246, W.273, R.293, E.308, H.309, L.335, R.338, R.339 Ligands: ASG-GCD.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.220, A:E.308 Water bridges: A:R.246, A:R.246, A:R.293, A:R.293, A:E.308, A:R.338, A:R.338 Salt bridges: A:R.246, A:R.293, A:H.309, A:H.309, A:R.338, A:R.339, A:R.293, A:R.338 ASG-GCD.3: 17 residues within 4Å: Chain A: H.91, Q.150, R.159, N.188, A.189, G.190, R.194, Y.197, E.220, T.223, K.225, R.246, H.247, E.308 Ligands: ASG-GCD.2, ASG-GCD.4, CA.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.150, A:R.159, A:A.189, A:K.225, A:N.188, A:N.188, A:T.223, A:K.225, A:E.308 Water bridges: A:D.149, A:Y.197 Salt bridges: A:H.91, A:H.91, A:R.159, A:R.194, A:K.225, A:K.225 ASG-GCD.4: 7 residues within 4Å: Chain A: F.148, P.186, G.187, N.188, A.189, N.478 Ligands: ASG-GCD.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.148 Hydrogen bonds: A:N.188, A:N.188, A:N.478 Water bridges: A:S.90, A:S.90

1 x NGK- GCD: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-alpha-D-galactopyranose(Non-covalent)

NGK-GCD.5: 9 residues within 4Å: Chain A: Y.102, N.103, H.134, C.135, R.136, Y.172, H.173, R.174, G.422 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.134, A:H.134 Water bridges: A:H.134, A:R.136, A:R.136, A:R.136, A:G.422 Salt bridges: A:R.136, A:R.174

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: N.188, E.218, E.220 Ligands: ASG-GCD.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.218, A:E.218, A:E.220, H2O.29, H2O.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Michel, G. et al., The Structure of Chondroitin B Lyase Complexed with Glycosaminoglycan Oligosaccharides Unravels a Calcium-Dependent Catalytic Machinery. J.Biol.Chem. (2004)

Release Date

2004-06-10

Peptides

CHONDROITINASE B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CHONDROITINASE B

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