SMTL ID : 6ptk.1 (1 other biounit)

Crystal structure of the sulfatase PsS1_NC C84A with bound sulfate ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 12 residues within 4Å: Chain A: D.35, D.36, L.73, A.74, N.95, K.129, H.131, H.229, Q.324, K.336 Ligands: GOL.7, CA.9 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.36, A:A.74, A:N.95, A:N.95 Water bridges: A:K.129 Salt bridges: A:K.129, A:H.131, A:H.229, A:K.336 SO4.15: 12 residues within 4Å: Chain B: D.35, D.36, L.73, A.74, N.95, K.129, H.131, H.229, Q.324, K.336 Ligands: GOL.18, CA.19 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:A.74, B:N.95, B:Q.324 Water bridges: B:K.129, B:H.229 Salt bridges: B:K.129, B:H.131, B:H.229, B:K.336 SO4.23: 12 residues within 4Å: Chain C: D.35, D.36, L.73, A.74, N.95, K.129, H.131, H.229, Q.324, K.336 Ligands: GOL.29, CA.31 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.36, C:A.74, C:N.95, C:N.95 Water bridges: C:K.129 Salt bridges: C:K.129, C:H.131, C:H.229, C:K.336 SO4.37: 12 residues within 4Å: Chain D: D.35, D.36, L.73, A.74, N.95, K.129, H.131, H.229, Q.324, K.336 Ligands: GOL.40, CA.41 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:A.74, D:N.95, D:Q.324 Water bridges: D:K.129, D:H.229 Salt bridges: D:K.129, D:H.131, D:H.229, D:K.336

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

9RN.2: 4 residues within 4Å: Chain A: L.108, S.109, K.115 Ligands: G4S.3 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:N.490, B:N.490, B:N.490 Hydrogen bonds: A:K.115 9RN.21: 4 residues within 4Å: Chain B: L.108, S.109, K.115 Ligands: G4S.22 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:N.490, A:N.490 Hydrogen bonds: B:K.115 9RN.24: 4 residues within 4Å: Chain C: L.108, S.109, K.115 Ligands: G4S.25 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.115 Water bridges: D:N.490, D:N.490, D:N.490 9RN.43: 4 residues within 4Å: Chain D: L.108, S.109, K.115 Ligands: G4S.44 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:N.490, C:N.490 Hydrogen bonds: D:K.115

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

G4S.3: 10 residues within 4Å: Chain A: S.109, G.111, S.112, K.115, R.116, S.119, D.383 Chain B: N.479 Ligands: 9RN.2, GOL.8 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.109, A:K.115, A:S.119, B:N.479 Water bridges: A:G.111, A:S.112 Salt bridges: A:K.115 G4S.22: 9 residues within 4Å: Chain A: N.479 Chain B: S.109, G.111, S.112, K.115, R.116, D.383 Ligands: GOL.13, 9RN.21 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.109, B:K.115, B:K.115, A:N.479 Water bridges: B:S.112, A:N.490, A:N.490 Salt bridges: B:K.115 G4S.25: 10 residues within 4Å: Chain C: S.109, G.111, S.112, K.115, R.116, S.119, D.383 Chain D: N.479 Ligands: 9RN.24, GOL.30 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.109, C:K.115, C:S.119, D:N.479 Water bridges: C:G.111, C:D.383 Salt bridges: C:K.115 G4S.44: 9 residues within 4Å: Chain C: N.479 Chain D: S.109, G.111, S.112, K.115, R.116, D.383 Ligands: GOL.35, 9RN.43 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:N.479, D:S.109, D:K.115, D:K.115 Water bridges: C:N.490, C:N.490, D:S.112, D:D.383 Salt bridges: D:K.115

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

EDO.4: 7 residues within 4Å: Chain A: G.128, K.129, W.146, G.147, H.148, E.201, E.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.128, A:H.148 EDO.5: 7 residues within 4Å: Chain A: W.86, G.87, H.88, D.93, A.412, E.414, R.424 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.88, A:H.88 Water bridges: A:G.87, A:D.93, A:D.93 EDO.6: 5 residues within 4Å: Chain A: P.158, F.159, T.160, Y.162 Chain C: S.440 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:S.440, C:S.440, A:T.160 Water bridges: A:T.160, A:Y.162 EDO.16: 6 residues within 4Å: Chain B: W.86, G.87, H.88, D.93, E.414, R.424 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.88, B:H.88 Water bridges: B:G.87 EDO.17: 6 residues within 4Å: Chain B: T.90, G.91, L.92, E.105, L.106, S.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.107 EDO.26: 7 residues within 4Å: Chain C: G.128, K.129, W.146, G.147, H.148, E.201, E.226 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.128, C:H.148, C:E.201 Water bridges: C:E.226 EDO.27: 7 residues within 4Å: Chain C: W.86, G.87, H.88, D.93, A.412, E.414, R.424 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.88 Water bridges: C:G.87, C:D.93 EDO.28: 5 residues within 4Å: Chain A: S.440 Chain C: P.158, F.159, T.160, Y.162 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:S.440, A:S.440, C:T.160, C:T.160 Water bridges: C:T.160, C:Y.162 EDO.38: 6 residues within 4Å: Chain D: W.86, G.87, H.88, D.93, E.414, R.424 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.88, D:H.88 Water bridges: D:G.87 EDO.39: 6 residues within 4Å: Chain D: T.90, G.91, L.92, E.105, L.106, S.107 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.107

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 10 residues within 4Å: Chain A: N.95, L.98, H.229, W.269, W.271, D.335, K.336, Y.416, N.417 Ligands: SO4.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.95, A:D.335, A:K.336, A:N.417 Water bridges: A:H.229, A:H.229 GOL.8: 8 residues within 4Å: Chain A: R.85, S.109, E.110, D.383 Chain B: N.479, D.482 Ligands: G4S.3, CA.14 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.479 Water bridges: B:D.482, B:D.482, A:S.109 GOL.13: 8 residues within 4Å: Chain A: N.479, D.482 Chain B: R.85, S.109, E.110, D.383 Ligands: CA.10, G4S.22 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.109, B:S.109, A:N.479 GOL.18: 10 residues within 4Å: Chain B: N.95, L.98, H.229, W.269, W.271, D.335, K.336, Y.416, N.417 Ligands: SO4.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.95, B:D.335, B:Y.416, B:N.417 Water bridges: B:H.229 GOL.29: 10 residues within 4Å: Chain C: N.95, L.98, H.229, W.269, W.271, D.335, K.336, Y.416, N.417 Ligands: SO4.23 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.95, C:D.335, C:K.336, C:Y.416, C:N.417 Water bridges: C:H.229 GOL.30: 8 residues within 4Å: Chain C: R.85, S.109, E.110, D.383 Chain D: N.479, D.482 Ligands: G4S.25, CA.36 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.479 Water bridges: D:D.482, D:D.482, D:D.482, D:D.482, D:D.482, D:D.482, D:D.482, C:S.109 GOL.35: 8 residues within 4Å: Chain C: N.479, D.482 Chain D: R.85, S.109, E.110, D.383 Ligands: CA.32, G4S.44 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.109, D:S.109, C:N.479 Water bridges: D:E.110 GOL.40: 10 residues within 4Å: Chain D: N.95, L.98, H.229, W.269, W.271, D.335, K.336, Y.416, N.417 Ligands: SO4.37 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.95, D:D.335, D:Y.416, D:Y.416, D:N.417 Water bridges: D:H.229

14 x CA: CALCIUM ION(Non-covalent)

CA.9: 6 residues within 4Å: Chain A: D.35, D.36, A.74, D.323, Q.324 Ligands: SO4.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.35, A:D.36, A:D.323, A:D.323 CA.10: 4 residues within 4Å: Chain A: N.479, D.482 Chain B: D.383 Ligands: GOL.13 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:N.479, A:D.482, B:D.383, H2O.14 CA.11: 2 residues within 4Å: Chain A: D.385 Chain B: D.385 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.385, H2O.7, H2O.10, H2O.23, H2O.32 CA.12: 5 residues within 4Å: Chain A: T.196, V.197, T.198, Q.227, M.295 No protein-ligand interaction detected (PLIP) CA.14: 4 residues within 4Å: Chain A: D.383 Chain B: N.479, D.482 Ligands: GOL.8 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:N.479, B:D.482, A:D.383, H2O.14 CA.19: 6 residues within 4Å: Chain B: D.35, D.36, A.74, D.323, Q.324 Ligands: SO4.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.35, B:D.36, B:D.323, B:D.323 CA.20: 5 residues within 4Å: Chain B: T.196, V.197, T.198, Q.227, M.295 No protein-ligand interaction detected (PLIP) CA.31: 6 residues within 4Å: Chain C: D.35, D.36, A.74, D.323, Q.324 Ligands: SO4.23 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.35, C:D.36, C:D.323, C:D.323 CA.32: 4 residues within 4Å: Chain C: N.479, D.482 Chain D: D.383 Ligands: GOL.35 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:N.479, C:D.482, D:D.383, H2O.50 CA.33: 2 residues within 4Å: Chain C: D.385 Chain D: D.385 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.385, H2O.42, H2O.45, H2O.58, H2O.67 CA.34: 5 residues within 4Å: Chain C: T.196, V.197, T.198, Q.227, M.295 No protein-ligand interaction detected (PLIP) CA.36: 4 residues within 4Å: Chain C: D.383 Chain D: N.479, D.482 Ligands: GOL.30 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:D.383, D:N.479, D:D.482, H2O.49 CA.41: 6 residues within 4Å: Chain D: D.35, D.36, A.74, D.323, Q.324 Ligands: SO4.37 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.35, D:D.36, D:D.323, D:D.323 CA.42: 5 residues within 4Å: Chain D: T.196, V.197, T.198, Q.227, M.295 No protein-ligand interaction detected (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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

exo-2S-iota carrageenan S1 sulfatase

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