SMTL ID : 6g5z.1

Choline sulfatase from Ensifer (Sinorhizobium) meliloti

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 8 residues within 4Å: Chain A: D.10, A.50, R.54, K.98, H.197, D.292, H.293, K.305 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.10, A:D.10, A:D.292, A:H.293 MG.7: 8 residues within 4Å: Chain B: D.10, A.50, R.54, K.98, H.197, D.292, H.293 Ligands: SO4.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.10, B:D.10, B:D.292, B:H.293 MG.14: 8 residues within 4Å: Chain C: D.10, A.50, R.54, K.98, H.197, D.292, H.293 Ligands: SO4.16 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.10, C:D.10, C:D.292, C:H.293 MG.17: 7 residues within 4Å: Chain D: D.10, A.50, R.54, H.197, D.292, H.293 Ligands: SO4.18 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.10, D:D.10, D:D.292, D:H.293

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: Y.400, R.441, W.445, D.446, M.447, E.448 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.447, A:E.448 Salt bridges: A:R.441 SO4.3: 5 residues within 4Å: Chain A: R.67, Q.76, R.460 Chain C: R.67, Q.76 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Water bridges: C:Q.76, A:R.67, A:R.67 Salt bridges: C:R.67, A:R.67 SO4.4: 3 residues within 4Å: Chain A: H.329, L.330, T.331 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.330, A:T.331, A:T.331, A:T.331 Salt bridges: A:H.329 SO4.5: 4 residues within 4Å: Chain A: H.215, P.218, E.219, R.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.219 Water bridges: A:R.255, A:R.255 Salt bridges: A:R.255 SO4.6: 9 residues within 4Å: Chain A: L.49, A.50, N.71, K.98, H.100, Y.119, W.125, H.197, K.305 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.71 Water bridges: A:Y.119 Salt bridges: A:K.98, A:H.100, A:H.197, A:K.305 SO4.8: 5 residues within 4Å: Chain B: L.328, H.329, L.330, T.331, M.365 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.330, B:T.331, B:T.331 SO4.9: 6 residues within 4Å: Chain B: Y.400, R.441, W.445, D.446, M.447, E.448 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.447, B:E.448 Water bridges: B:W.445 Salt bridges: B:R.441 SO4.10: 5 residues within 4Å: Chain B: L.25, H.26, A.27, P.28, K.31 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.27 Salt bridges: B:H.26, B:K.31 SO4.11: 3 residues within 4Å: Chain B: Q.431, L.434, R.438 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.431, B:Q.431 Salt bridges: B:R.438 SO4.12: 4 residues within 4Å: Chain B: P.224, L.225, M.236, Y.241 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.225, B:Y.241 SO4.13: 11 residues within 4Å: Chain B: L.49, A.50, N.71, K.98, H.100, Y.119, W.125, H.141, H.197, K.305 Ligands: MG.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.71 Salt bridges: B:K.98, B:H.100, B:H.197, B:K.305 SO4.15: 5 residues within 4Å: Chain C: L.328, H.329, L.330, T.331, M.365 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.328, C:L.330, C:T.331, C:T.331, C:T.331 SO4.16: 11 residues within 4Å: Chain C: L.49, A.50, N.71, K.98, H.100, Y.119, W.125, H.141, H.197, K.305 Ligands: MG.14 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.71, C:N.71 Water bridges: C:Y.119 Salt bridges: C:K.98, C:H.100, C:H.197, C:K.305 SO4.18: 10 residues within 4Å: Chain D: L.49, A.50, N.71, H.100, Y.119, W.125, H.141, H.197, K.305 Ligands: MG.17 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.71 Salt bridges: D:H.100, D:H.141, D:H.197, D:K.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gavira, J.A. et al., Structural insights into choline-O-sulfatase reveal the molecular determinants for ligand binding. Acta Crystallogr D Struct Biol (2022)

Release Date

2019-04-10

Peptides

Choline-sulfatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Choline-sulfatase

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