SMTL ID : 6pt4.1

Crystal structure of apo PsS1_NC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.35, D.36, C.74, D.323, Q.324, K.336 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.35, A:D.36, A:D.323, A:D.323 CA.8: 5 residues within 4Å: Chain B: D.35, D.36, C.74, D.323, Q.324 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.35, B:D.36, B:D.323, B:D.323

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

EDO.2: 7 residues within 4Å: Chain A: W.86, G.87, H.88, D.93, A.412, E.414, R.424 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.88, A:H.88 Water bridges: A:G.87, A:D.93 EDO.3: 5 residues within 4Å: Chain A: Q.227, H.229, P.231, R.233 Ligands: CL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.233 Water bridges: A:H.229, A:R.233, A:R.233 EDO.4: 6 residues within 4Å: Chain A: N.95, L.98, W.269, W.271, Y.416, N.417 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.95, A:Y.416, A:N.417 EDO.9: 6 residues within 4Å: Chain A: D.266, I.267, W.268 Chain B: D.266, I.267, W.268 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:I.267, A:I.267 Water bridges: B:D.266, B:I.267, B:I.267, A:I.267, A:I.267 EDO.10: 7 residues within 4Å: Chain B: W.86, G.87, H.88, D.93, A.412, E.414, R.424 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.88, B:H.88 Water bridges: B:G.87, B:D.93 EDO.11: 4 residues within 4Å: Chain B: K.200, N.203, E.204 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.203 Water bridges: B:K.200, B:K.200 EDO.12: 5 residues within 4Å: Chain B: Q.227, H.229, P.231, R.233 Ligands: CL.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.233 Water bridges: B:R.233 EDO.13: 4 residues within 4Å: Chain B: M.145, E.204, L.207 Ligands: EDO.11 No protein-ligand interaction detected (PLIP) EDO.14: 2 residues within 4Å: Chain B: N.305, E.309 No protein-ligand interaction detected (PLIP) EDO.15: 8 residues within 4Å: Chain B: D.35, D.36, C.74, H.229, P.230, W.271, D.335, K.336 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.35, B:H.229, B:D.335, B:K.336 EDO.16: 4 residues within 4Å: Chain B: A.138, F.144, K.150, D.151 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.151 Water bridges: B:F.144

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

CL.5: 6 residues within 4Å: Chain A: T.196, V.197, T.198, Q.227, M.295 Ligands: EDO.3 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: Q.376, L.392, P.393, K.396 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: I.255, R.257, K.260, H.331 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain B: T.196, V.197, T.198, Q.227, M.295 Ligands: EDO.12 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: I.255, R.257, K.260, H.331 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: Q.376, L.392, P.393, K.396 Ligand excluded by PLIP

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-2S-iota carrageenan S1 sulfatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

exo-2S-iota carrageenan S1 sulfatase