SMTL ID : 6byp.1 (1 other biounit)

Structure of PL24 family Polysaccharide lyase-LOR107

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: D.198, D.208, K.210 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.198, A:D.208, H2O.2, H2O.4, H2O.8 CA.2: 3 residues within 4Å: Chain A: N.309, D.312, F.314 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.309, A:F.314, H2O.5, H2O.6, H2O.8

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: H.363, T.364, A.365, S.368, R.398 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.364, A:A.365, A:S.368, A:S.368 Water bridges: A:R.398 Salt bridges: A:H.363, A:R.398 SO4.4: 3 residues within 4Å: Chain A: D.311, D.312, R.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.311, A:R.313 Salt bridges: A:R.313 SO4.5: 3 residues within 4Å: Chain A: H.370, T.373, R.392 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.373 Water bridges: A:V.372 Salt bridges: A:H.370, A:R.392 SO4.6: 1 residues within 4Å: Chain A: R.118 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.96, A:R.118 Salt bridges: A:R.118 SO4.7: 5 residues within 4Å: Chain A: P.116, H.117, Q.204, D.207, K.210 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.117, A:D.207 Water bridges: A:H.117, A:R.118, A:R.118, A:Y.209, A:K.210, A:K.210 Salt bridges: A:K.210 SO4.8: 4 residues within 4Å: Chain A: F.122, R.123, H.153, R.163 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.123, A:H.153, A:R.163 SO4.9: 4 residues within 4Å: Chain A: H.132, Y.229, R.245, Y.289 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.229, A:N.249 Salt bridges: A:H.132, A:R.245 SO4.10: 4 residues within 4Å: Chain A: N.69, H.73, H.472, G.473 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.69 Water bridges: A:G.473, A:G.473, A:G.473 Salt bridges: A:H.73

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 10 residues within 4Å: Chain A: Y.175, F.177, H.211, T.213, M.214, T.215, G.216, Q.264, K.265, W.266 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.216, A:Q.264 Water bridges: A:Y.175, A:L.212, A:L.212 GOL.12: 3 residues within 4Å: Chain A: N.249, N.250, N.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.249, A:N.250, A:N.310 GOL.13: 5 residues within 4Å: Chain A: N.97, Q.114, F.115, P.116, L.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.114, A:Q.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ulaganathan, T. et al., Structure-function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism. J. Biol. Chem. (2018)

Release Date

2018-02-07

Peptides

Short ulvan lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Short ulvan lyase

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