SMTL ID : 7ptj.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

5 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 14 residues within 4Å: Chain A: L.53, S.54, N.75, H.104, Y.123, W.129, W.142, W.143, Y.144, H.145, N.146, H.201, K.309 Ligands: CA.10 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.54, A:N.75, A:N.75, A:Y.144, A:N.146 Water bridges: A:N.146 Salt bridges: A:H.104, A:H.201, A:K.309 EPE.2: 8 residues within 4Å: Chain A: D.27, F.28, L.29, H.30, A.31, P.32, K.35, D.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.31 Salt bridges: A:H.30, A:K.35, A:D.216 EPE.12: 14 residues within 4Å: Chain B: L.53, S.54, N.75, H.104, Y.123, W.129, W.142, W.143, Y.144, H.145, N.146, H.201, K.309 Ligands: CA.21 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.54, B:N.75 Salt bridges: B:H.104, B:H.201, B:K.309 EPE.22: 14 residues within 4Å: Chain C: L.53, S.54, N.75, H.104, Y.123, W.129, W.142, W.143, Y.144, H.145, N.146, H.201, K.309 Ligands: CA.35 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.54, C:S.54, C:N.75, C:Y.123, C:Y.144 Water bridges: C:H.145, C:N.146 Salt bridges: C:H.104, C:H.201, C:K.309 EPE.36: 13 residues within 4Å: Chain D: L.53, S.54, N.75, H.104, W.129, W.142, W.143, Y.144, H.145, N.146, H.201, K.309 Ligands: CA.39 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.54, D:N.75, D:Y.123, D:Y.144 Salt bridges: D:H.104, D:H.201, D:K.309

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

SO4.3: 5 residues within 4Å: Chain A: R.445, W.449, D.450, M.451, E.452 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.451, A:E.452 Salt bridges: A:R.445 SO4.4: 5 residues within 4Å: Chain A: R.430, G.431, P.432, V.433, D.434 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.433, A:D.434 Water bridges: A:R.430 SO4.5: 3 residues within 4Å: Chain A: P.228, L.229, Y.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.229, A:Y.245, A:Y.245 SO4.6: 2 residues within 4Å: Chain A: T.221, R.256 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.221 Water bridges: A:L.220, A:L.220, A:T.221, A:R.256 Salt bridges: A:R.256 SO4.11: 2 residues within 4Å: Chain A: R.71 Chain B: R.71 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Water bridges: A:R.71, A:R.71, A:R.71, A:Q.80, A:Q.80, B:R.71, B:Q.80, B:Q.80 Salt bridges: A:R.71, B:R.71 SO4.13: 3 residues within 4Å: Chain B: P.228, L.229, Y.245 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.229, B:Y.245 SO4.23: 3 residues within 4Å: Chain C: Q.435, L.438, R.442 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.435, C:Q.435 Water bridges: C:R.442, C:R.442, C:R.442 Salt bridges: C:R.442 SO4.24: 2 residues within 4Å: Chain C: R.71 Chain D: R.71 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Water bridges: C:R.71, C:Q.80, D:Q.80, D:Q.80 Salt bridges: C:R.71, D:R.71 SO4.25: 4 residues within 4Å: Chain C: W.449, D.450, M.451, E.452 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:M.451, C:E.452, C:E.452, C:E.452 Water bridges: C:R.445, C:R.445, C:R.445, C:A.446, C:W.449 SO4.26: 5 residues within 4Å: Chain C: E.397, W.400, A.440, F.441, M.444 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.400 SO4.27: 3 residues within 4Å: Chain C: P.228, L.229, M.240 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.229 Water bridges: C:D.230 SO4.37: 3 residues within 4Å: Chain D: P.228, L.229, Y.245 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.229 SO4.38: 5 residues within 4Å: Chain D: L.29, H.30, A.31, P.32, K.35 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.29, D:A.31 Water bridges: D:K.35 Salt bridges: D:H.30, D:K.35

17 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: N.17, K.19, E.223, R.259, M.300, L.301, E.303 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: W.211, E.215, L.220, E.253, R.256, R.257, R.260 Ligand excluded by PLIP GOL.9: 1 residues within 4Å: Chain A: R.71 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain B: H.333, M.369, G.372, V.373, E.374 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain B: N.17, K.19, L.20, E.223, R.259, M.300, L.301 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain B: A.390, A.406, L.407, D.455 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: W.211, L.220, E.253, R.256, R.257, R.260 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: L.334, P.336, R.396, G.398, K.399, E.416 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain B: V.155, R.208, W.211, R.257, R.260 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: L.29, H.30, A.31, P.32, K.35 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain C: N.17, K.19, L.20, E.223, R.259 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain C: W.211, E.215, L.220, E.253, R.256, R.260 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain C: L.29, H.30, A.31, P.32, K.35 Ligand excluded by PLIP GOL.31: 3 residues within 4Å: Chain C: W.449, D.450, F.454 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain C: S.353, L.354, E.355 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain C: L.332, H.333, L.334, T.335, M.369 Ligand excluded by PLIP GOL.34: 4 residues within 4Å: Chain C: Y.96, L.179, E.182, R.189 Ligand excluded by PLIP

4 x CA: CALCIUM ION(Non-covalent)

CA.10: 7 residues within 4Å: Chain A: D.14, S.54, K.102, H.201, D.296, H.297 Ligands: EPE.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.14, A:D.14, A:S.54 CA.21: 6 residues within 4Å: Chain B: D.14, S.54, H.201, D.296, H.297 Ligands: EPE.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.14, B:S.54 CA.35: 6 residues within 4Å: Chain C: D.14, S.54, H.201, D.296, H.297 Ligands: EPE.22 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.14, C:D.14, C:S.54, C:D.296, C:H.297 CA.39: 6 residues within 4Å: Chain D: D.14, S.54, H.201, D.296, H.297 Ligands: EPE.36 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.14, D:D.14, D:D.296

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
A

B
B

C
C

D
D

Choline sulfatase

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