SMTL ID : 5gkd.1 (2 other biounits)

Structure of PL6 family alginate lyase AlyGC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: N.180, E.183, E.212, E.214 Ligands: PO4.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.183, A:E.212, A:E.212, A:E.214, H2O.2 CA.10: 5 residues within 4Å: Chain B: N.180, E.183, E.212, E.214 Ligands: PO4.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.183, B:E.212, B:E.212, B:E.214, H2O.33

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: T.189, S.190, K.219, N.301 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.189, A:S.190, A:S.190, A:S.190, A:K.219, A:N.301 GOL.7: 6 residues within 4Å: Chain A: K.6, A.27, N.28, G.29, T.30, W.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.31 Water bridges: A:K.6 GOL.8: 6 residues within 4Å: Chain A: D.420, E.421, V.422, G.423, V.424, S.425 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.421 Water bridges: A:K.429, A:K.429 GOL.9: 2 residues within 4Å: Chain A: Y.574, Y.606 No protein-ligand interaction detected (PLIP) GOL.11: 4 residues within 4Å: Chain B: T.189, S.190, K.219, N.301 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.190, B:S.190, B:S.190, B:K.219, B:N.301 Water bridges: B:K.219 GOL.16: 5 residues within 4Å: Chain B: K.6, N.28, G.29, T.30, W.31 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.30 GOL.17: 7 residues within 4Å: Chain B: D.420, E.421, V.422, G.423, V.424, S.425, K.429 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.421 Water bridges: B:K.419, B:S.425, B:S.425, B:K.429 GOL.18: 2 residues within 4Å: Chain B: Y.574, Y.606 No protein-ligand interaction detected (PLIP)

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

PO4.3: 3 residues within 4Å: Chain A: R.94, Y.129, R.153 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.129 Water bridges: A:R.94, A:R.94, A:R.94, A:R.153, B:Q.498 Salt bridges: A:R.94, A:R.153 PO4.4: 8 residues within 4Å: Chain A: N.180, E.183, E.214, S.217, K.219, R.240 Ligands: CA.1, CO3.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.180, A:E.183, A:S.217 Water bridges: A:N.180, A:N.180, A:E.183, A:R.240, A:R.240, A:R.240 Salt bridges: A:K.219, A:R.240 PO4.5: 3 residues within 4Å: Chain A: R.67, R.95 Chain B: D.448 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Water bridges: A:R.67, A:R.67, A:R.95, A:R.95, A:N.96 Salt bridges: A:R.67, A:R.95 Hydrogen bonds: B:D.448 PO4.12: 2 residues within 4Å: Chain B: R.94, R.153 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.94, B:R.94 Salt bridges: B:R.94, B:R.153 PO4.13: 8 residues within 4Å: Chain B: N.180, E.183, E.214, S.217, K.219, R.240 Ligands: CA.10, CO3.15 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.180, B:S.217, B:S.217 Water bridges: B:N.180, B:E.214, B:S.217, B:K.219, B:R.240, B:R.240, B:R.240 Salt bridges: B:K.219, B:R.240 PO4.14: 2 residues within 4Å: Chain B: R.67, R.95 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.67, B:R.67 Salt bridges: B:R.67, B:R.95

2 x CO3: CARBONATE ION(Non-functional Binders)

CO3.6: 5 residues within 4Å: Chain A: E.214, R.240, R.264, Y.303 Ligands: PO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.264, A:R.264, A:Y.303 CO3.15: 5 residues within 4Å: Chain B: E.214, R.240, R.264, Y.303 Ligands: PO4.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.214, B:R.240, B:Y.303, B:Y.303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, F. et al., Novel Molecular Insights into the Catalytic Mechanism of Marine Bacterial Alginate Lyase AlyGC from Polysaccharide Lyase Family 6. J. Biol. Chem. (2017)

Release Date

2017-02-08

Peptides

AlyGC: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

AlyGC

Related Entries With Identical Sequence