SMTL ID : 6byp.2 (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: 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.3, H2O.5, H2O.6 CA.2: 3 residues within 4Å: Chain A: D.198, D.208, K.210 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.198, A:D.208, A:D.208, A:K.210, H2O.10

6 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 Water bridges: A:R.398, 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.313 Water bridges: A:R.313, A:R.313 Salt bridges: A:R.313 SO4.5: 5 residues within 4Å: Chain A: F.66, 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 SO4.6: 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:H.132, A:Y.289, A:Y.289 Salt bridges: A:R.245 SO4.7: 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:H.370 Salt bridges: A:H.370, A:R.392 SO4.8: 4 residues within 4Å: Chain A: N.69, H.73, H.472, G.473 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.69 Water bridges: A:G.473 Salt bridges: A:H.73

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: Y.360, I.419, T.420, T.421, D.422 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.420, A:T.420, A:T.421 GOL.10: 5 residues within 4Å: Chain A: G.281, N.282, V.347, N.348, E.351 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.348, A:N.348 Water bridges: A:T.343, A:N.348

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

PEG.11: 5 residues within 4Å: Chain A: L.30, Q.33, Q.464, A.465, S.466 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.33, A:A.465, A:S.466 Water bridges: A:Q.33, A:Q.464

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
B

Short ulvan lyase

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