SMTL ID : 6psm.2 (2 other biounits)

Crystal structure of PsS1_19B C77S in complex with kappa-neocarrabiose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.33, D.34, S.73, D.286, N.287, K.305 Ligands: G4S.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.33, A:D.34, A:D.286, A:D.286 CA.6: 7 residues within 4Å: Chain B: D.33, D.34, S.73, D.286, N.287, K.305 Ligands: G4S.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.33, B:D.34, B:D.286, B:D.286

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

CL.2: 5 residues within 4Å: Chain A: K.293, K.305, R.458 Ligands: G4S.4, 9RN.5 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: K.293, K.305, R.458 Ligands: G4S.11, 9RN.12 Ligand excluded by PLIP

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

EDO.3: 5 residues within 4Å: Chain A: L.115, Q.117, D.122, K.149, R.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.122, A:R.150 EDO.10: 5 residues within 4Å: Chain B: L.115, Q.117, D.122, K.149, R.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.122, B:R.150

2 x G4S: 4-O-sulfo-beta-D-galactopyranose(Non-covalent)

G4S.4: 15 residues within 4Å: Chain A: D.33, D.34, S.73, I.94, K.136, H.138, G.161, D.162, H.229, T.230, K.293, K.305 Ligands: CA.1, CL.2, 9RN.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.73, A:S.73, A:G.161, A:D.162, A:N.287, A:K.293, A:K.293, A:K.305 Water bridges: A:G.161 Salt bridges: A:K.136, A:H.138, A:H.229, A:H.229, A:K.305, A:K.305 G4S.11: 16 residues within 4Å: Chain B: D.33, D.34, S.73, I.94, K.136, H.138, G.161, D.162, H.229, T.230, N.287, K.293, K.305 Ligands: CA.6, CL.7, 9RN.12 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.73, B:S.73, B:G.161, B:T.230, B:N.287, B:K.293, B:K.293, B:K.305 Salt bridges: B:K.136, B:H.138, B:H.229, B:H.229, B:K.305, B:K.305

2 x 9RN: 3,6-anhydro-D-galactose(Non-covalent)

9RN.5: 10 residues within 4Å: Chain A: I.94, F.99, K.305, S.306, Y.451, Y.454, D.455, R.458 Ligands: CL.2, G4S.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.305, A:S.306, A:S.306, A:Y.451, A:R.458 9RN.12: 10 residues within 4Å: Chain B: I.94, F.99, K.305, S.306, Y.451, Y.454, D.455, R.458 Ligands: CL.7, G4S.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.305, B:Y.451, B:R.458

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 3 residues within 4Å: Chain B: D.276, D.277 Ligands: ZN.9 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.276, H2O.9 ZN.9: 3 residues within 4Å: Chain B: D.276, D.277 Ligands: ZN.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hettle, A.G. et al., Insights into the kappa / iota-carrageenan metabolism pathway of some marinePseudoalteromonasspecies. Commun Biol (2019)

Release Date

2019-09-25

Peptides

exo-4S-kappa carrageenan S1 sulfatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

exo-4S-kappa carrageenan S1 sulfatase

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