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

Complex structure of LOR107 mutant (R320) with tetrasaccharide substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x 83Y- BDP- 83Y- GCD: 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-rhamnopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-rhamnopyranose

83Y-BDP-83Y-GCD.1: 15 residues within 4Å: Chain A: F.56, G.57, H.63, F.112, R.113, S.121, H.122, H.143, R.153, Y.219, G.237, G.238, N.239, Y.279, T.363 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.121, A:Y.219, A:Y.219, A:N.239, A:Y.279 Salt bridges: A:H.63, A:H.122, A:H.122, A:H.143

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: D.188, D.198, K.200 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.188, A:D.198, A:K.200, H2O.1, H2O.5 CA.3: 3 residues within 4Å: Chain A: N.299, D.302, F.304 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:N.299, A:D.302, A:F.304, H2O.2, H2O.4

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

SO4.4: 5 residues within 4Å: Chain A: H.353, T.354, A.355, S.358, R.388 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.354, A:A.355 Salt bridges: A:H.353, A:R.388 SO4.5: 3 residues within 4Å: Chain A: D.302, R.303, T.354 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.303 Salt bridges: A:R.303 SO4.6: 3 residues within 4Å: Chain A: H.360, T.363, R.382 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.363, A:T.363 Water bridges: A:V.362 Salt bridges: A:H.360, A:R.382

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: E.371, G.423, D.424 No protein-ligand interaction detected (PLIP)

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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