SMTL ID : 2wda.1

The X-ray structure of the Streptomyces coelicolor A3 Chondroitin AC Lyase in Complex with Chondroitin sulphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 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.1: 12 residues within 4Å: Chain A: W.141, E.142, R.149, T.252, Y.253, V.256, R.307, R.311, E.434 Ligands: FMT.2, GOL.9, PEG.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.253 Hydrogen bonds: A:E.142, A:Y.253, A:Y.253, A:R.311, A:R.311, A:R.311 Water bridges: A:E.142, A:R.307, A:N.432 Salt bridges: A:R.307, A:R.311, A:R.149

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 7 residues within 4Å: Chain A: W.140, W.141, N.194, H.244, Y.253 Ligands: ASG-GCD.1, GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.194, A:Y.253 FMT.3: 2 residues within 4Å: Chain A: W.95, D.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.153 Water bridges: A:R.200, A:R.200 FMT.4: 6 residues within 4Å: Chain A: R.53, T.57, E.99, Q.103, P.374, V.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.57, A:V.375 Water bridges: A:T.38, A:L.39 FMT.5: 5 residues within 4Å: Chain A: D.456, D.460, N.557, L.558, G.559 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.456, A:D.460, A:Q.564 Water bridges: A:Q.457 FMT.6: 7 residues within 4Å: Chain A: R.406, M.420, A.426, H.427, Y.428, T.441, G.442 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.406, A:R.406, A:T.441, A:T.441

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: H.427, K.493, P.494, D.495, K.515, G.516, S.519 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.427, A:D.495, A:S.519, A:S.519 Water bridges: A:D.495, A:K.515, A:G.516 GOL.8: 5 residues within 4Å: Chain A: L.400, T.503, C.755, T.756, T.757 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.757, A:T.757, A:T.757 GOL.9: 8 residues within 4Å: Chain A: N.139, W.140, W.141, R.307, N.432, W.489 Ligands: ASG-GCD.1, FMT.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.139, A:W.140, A:R.307, A:N.432 Water bridges: A:H.244

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 4 residues within 4Å: Chain A: D.175, P.179, D.180, K.214 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.180, A:D.180, A:K.214 Water bridges: A:A.181 PEG.11: 10 residues within 4Å: Chain A: W.141, R.149, D.197, R.200, Y.253, Q.255, V.256, D.259 Ligands: ASG-GCD.1, ASG-GCD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.149, A:R.149, A:Q.255, A:D.259, A:D.259 Water bridges: A:D.197, A:R.200 PEG.12: 6 residues within 4Å: Chain A: A.450, H.574, E.576, G.577, G.638, A.639 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.577 Water bridges: A:R.641 PEG.13: 8 residues within 4Å: Chain A: D.467, Y.469, R.470, V.476, T.478, R.480, E.550 Ligands: PEG.18 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.480, A:R.480, A:E.550 Water bridges: A:R.470, A:R.595 PEG.14: 6 residues within 4Å: Chain A: R.437, T.465, V.466, D.467, W.468, R.595 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.595 Water bridges: A:R.437 PEG.15: 7 residues within 4Å: Chain A: T.230, K.231, G.232, Y.236, A.403, R.424, V.754 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.232, A:Y.236, A:R.424 Water bridges: A:T.245, A:R.713 PEG.16: 4 residues within 4Å: Chain A: R.589, T.590, L.591 Ligands: PEG.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.590 Water bridges: A:T.590 PEG.17: 8 residues within 4Å: Chain A: Q.564, A.565, L.566, T.590, L.591, R.592, Q.616 Ligands: PEG.16 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.566, A:T.590, A:Q.616 Water bridges: A:T.590, A:R.592 PEG.18: 10 residues within 4Å: Chain A: V.466, D.467, R.470, N.555, L.591, E.593, R.595, W.615, T.617 Ligands: PEG.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.467, A:D.467, A:R.470, A:N.555 Water bridges: A:R.595

1 x MG: MAGNESIUM ION(Non-covalent)

MG.19: 4 residues within 4Å: Chain A: W.653, V.668, P.669, S.670 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:W.653, A:S.670, H2O.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Elmabrouk, Z.H. et al., Crystal Structures of a Family 8 Polysaccharide Lyase Reveal Open and Highly Occluded Substrate-Binding Cleft Conformations. Proteins (2011)

Release Date

2010-04-21

Peptides

PUTATIVE SECRETED LYASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PUTATIVE SECRETED LYASE

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