SMTL ID : 7pth.1

C54S mutant of choline-sulfatase from E. meliloti CECT4857 bound to choline

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x CHT: CHOLINE ION(Non-covalent)

CHT.1: 11 residues within 4Å: Chain A: L.53, N.75, Y.123, W.129, W.143, Y.144, H.145, H.201, K.309, E.386 Chain B: L.499 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.75, A:K.309 Water bridges: A:N.75, A:E.386 pi-Cation interactions: A:H.145 CHT.5: 13 residues within 4Å: Chain A: L.499 Chain B: L.53, S.54, N.75, H.104, Y.123, W.129, W.143, Y.144, H.145, H.201, K.309, E.386 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.75, B:K.309 Water bridges: B:N.75 pi-Cation interactions: B:H.145 CHT.8: 11 residues within 4Å: Chain C: L.53, N.75, Y.123, W.129, W.143, Y.144, H.145, H.201, K.309, E.386 Chain D: L.499 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.75, C:K.309, C:E.386, C:E.386 pi-Cation interactions: C:H.145 CHT.12: 11 residues within 4Å: Chain C: L.499 Chain D: L.53, N.75, Y.123, W.129, W.143, Y.144, H.145, H.201, K.309, E.386 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.75, D:K.309 Water bridges: D:N.75 pi-Cation interactions: D:H.145

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 7 residues within 4Å: Chain A: N.17, K.19, L.20, E.223, R.259, L.301, E.303 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.17, A:E.223, A:R.259 Salt bridges: A:R.259 ACT.3: 2 residues within 4Å: Chain A: D.27, F.28 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.27

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 9 residues within 4Å: Chain A: D.14, Q.15, S.54, R.58, K.102, H.201, D.296, H.297, K.309 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.14, A:D.14, A:D.296, A:H.297 CA.7: 8 residues within 4Å: Chain B: D.14, S.54, R.58, K.102, H.201, D.296, H.297, K.309 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.14, B:D.14, B:D.296, B:H.297 CA.11: 8 residues within 4Å: Chain C: D.14, S.54, R.58, K.102, H.201, D.296, H.297, K.309 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.14, C:D.14, C:D.296, C:H.297, H2O.56 CA.13: 7 residues within 4Å: Chain D: D.14, S.54, R.58, K.102, H.201, D.296, H.297 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.14, D:D.14, D:D.296, D:H.297

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

EDO.6: 7 residues within 4Å: Chain B: R.71, Y.73, A.457, E.460, S.461, R.464 Chain D: Q.80 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.460, B:S.461, B:R.464 EDO.9: 6 residues within 4Å: Chain C: W.211, L.220, E.253, R.256, R.257, R.260 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.253, C:E.253, C:R.256, C:R.260 Water bridges: C:R.257

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 5 residues within 4Å: Chain C: W.142 Chain D: N.495, H.496, M.497, N.498 No protein-ligand interaction detected (PLIP)

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

2022-08-03

Peptides

Choline sulfatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
C

D
A

Choline sulfatase

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