SMTL ID : 5uas.2 (1 other biounit)

Structure of a new family of Polysaccharide lyase PL25-Ulvanlyase bound to -[GlcA(1-4)Rha3S]-

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 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: 18 residues within 4Å: Chain A: N.36, K.94, D.97, N.98, N.99, K.101, H.119, H.134, Y.164, R.180, A.183, H.184, Y.222, H.254, T.256, F.305, K.330, T.331 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.36, A:D.97, A:N.98, A:N.99, A:Y.164, A:H.184, A:Y.222, A:Y.222, A:N.36, A:T.331 Water bridges: A:N.99, A:N.99, A:K.101, A:K.101, A:R.258, A:R.258, A:R.258, A:N.36, A:K.94, A:K.335, A:R.362, A:R.362, A:K.433 Salt bridges: A:K.101, A:H.119, A:R.180, A:H.184, A:K.335

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.184, H.240, C.242, H.254 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.184, A:H.240, A:C.242, A:H.254

1 x K: POTASSIUM ION(Non-covalent)

K.3: 1 residues within 4Å: Chain A: I.40 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: G.333, P.334, K.335, V.360, R.362 Ligand excluded by PLIP

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 4 residues within 4Å: Chain A: T.459, A.460, M.461, P.462 No protein-ligand interaction detected (PLIP) EDO.6: 8 residues within 4Å: Chain A: V.360, T.378, Y.379, N.380, A.385, V.386, S.412, F.413 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.379, A:N.380, A:F.413 Water bridges: A:S.412, A:F.413, A:K.433

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ulaganathan, T. et al., New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture. ACS Chem. Biol. (2017)

Release Date

2017-03-29

Peptides

UlvanLyase-PL25: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

UlvanLyase-PL25

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