SMTL ID : 5uam.1 (1 other biounit)

Structure of a new family of Polysaccharide lyase PL25-Ulvanlyase.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

CL.1: 6 residues within 4Å: Chain A: G.333, P.334, K.335, V.360, R.362 Ligands: EDO.6 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.184, H.240, C.242, H.254 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.184, A:H.240, A:C.242, A:H.254

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: H.99, H.119, T.163, Y.164, R.180, H.184, Y.222 Ligands: EDO.9 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.164, A:Y.222, A:Y.222 Water bridges: A:H.99, A:T.163, A:Y.164, A:R.180, A:H.184 Salt bridges: A:H.99, A:H.119, A:R.180, A:H.184

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 11 residues within 4Å: Chain A: N.275, V.276, E.277, E.279, E.292, K.293, T.294, M.295, W.342, W.347 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.275, A:E.292, A:W.347

1 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain A: A.39, I.40, F.305, R.362 No protein-ligand interaction detected (PLIP)

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

EDO.6: 9 residues within 4Å: Chain A: T.256, R.258, W.303, T.304, F.305, T.331, K.335, R.362 Ligands: CL.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.256, A:T.256, A:K.335 EDO.7: 7 residues within 4Å: Chain A: N.132, H.184, R.185, C.242, H.254 Ligands: ZN.2, EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.132 EDO.8: 5 residues within 4Å: Chain A: P.129, L.130, D.187, K.208, H.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.187, A:K.208 Water bridges: A:S.205 EDO.9: 7 residues within 4Å: Chain A: H.119, H.134, R.180, A.183, H.184 Ligands: PO4.3, EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.119, A:R.180, A:H.184, A:H.184 EDO.10: 10 residues within 4Å: Chain A: A.290, D.291, E.292, K.293, T.294, M.295, A.296, R.298, W.347 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.295, A:R.298, A:R.298 Water bridges: A:W.347 EDO.11: 6 residues within 4Å: Chain A: V.41, Y.164, Y.222, R.258, F.305, N.306 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.164, A:R.258, A:R.258 Water bridges: A:N.306, A:N.306, A:N.306

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

Ulvan Lyase-PL25: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ulvan Lyase-PL25

Related Entries With Identical Sequence