SMTL ID : 8eg3.1

Structure of human placental steroid (estrone/DHEA) sulfatase at 2.0 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-trimer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.35, D.36, A.75, D.342, Q.343 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.35, A:D.36, A:D.342, A:D.342 CA.7: 5 residues within 4Å: Chain B: D.35, D.36, A.75, D.342, Q.343 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.35, B:D.36, B:D.342, B:D.342 CA.13: 5 residues within 4Å: Chain C: D.35, D.36, A.75, D.342, Q.343 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.35, C:D.36, C:D.342, C:D.342

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 9 residues within 4Å: Chain A: G.40, D.41, N.47, I.50, Q.304, H.305, Y.308, S.360, G.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.304, A:H.305, A:S.360 NAG.3: 2 residues within 4Å: Chain A: R.330, N.333 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.330 Hydrogen bonds: A:N.333 NAG.8: 9 residues within 4Å: Chain B: G.40, D.41, N.47, I.50, Q.304, H.305, Y.308, S.360, G.362 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.304, B:H.305, B:S.360 NAG.9: 2 residues within 4Å: Chain B: R.330, N.333 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.330 Hydrogen bonds: B:N.333 NAG.14: 9 residues within 4Å: Chain C: G.40, D.41, N.47, I.50, Q.304, H.305, Y.308, S.360, G.362 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.304, C:H.305, C:S.360 NAG.15: 2 residues within 4Å: Chain C: R.330, N.333 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:R.330 Hydrogen bonds: C:N.333

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 2 residues within 4Å: Chain A: H.142, K.556 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.556, A:K.556, A:K.556 Salt bridges: A:H.142, A:K.556 PO4.10: 2 residues within 4Å: Chain B: H.142, K.556 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.556, B:K.556, B:K.556 Salt bridges: B:H.142, B:K.556 PO4.16: 2 residues within 4Å: Chain C: H.142, K.556 5 PLIP interactions: 5 interactions with chain C Water bridges: C:K.556, C:K.556, C:K.556 Salt bridges: C:H.142, C:K.556

6 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.5: 11 residues within 4Å: Chain A: K.144, Y.236, L.240, W.555, P.557, Q.560, L.561, C.562, L.568, C.570 Chain B: T.199 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.144, A:L.561 BOG.6: 11 residues within 4Å: Chain A: F.104, L.229, F.233, Y.236, F.237, L.240, N.241, W.555 Chain B: L.198, A.201, C.205 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.229, B:A.201 Hydrogen bonds: A:F.233, A:N.241, A:W.555 BOG.11: 11 residues within 4Å: Chain B: K.144, Y.236, L.240, W.555, P.557, Q.560, L.561, C.562, L.568, C.570 Chain C: T.199 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.144, B:L.561 BOG.12: 11 residues within 4Å: Chain B: F.104, L.229, F.233, Y.236, F.237, L.240, N.241, W.555 Chain C: L.198, A.201, C.205 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.229, C:A.201 Hydrogen bonds: B:F.233, B:N.241, B:W.555 BOG.17: 11 residues within 4Å: Chain A: T.199 Chain C: K.144, Y.236, L.240, W.555, P.557, Q.560, L.561, C.562, L.568, C.570 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.144, C:L.561 BOG.18: 11 residues within 4Å: Chain A: L.198, A.201, C.205 Chain C: F.104, L.229, F.233, Y.236, F.237, L.240, N.241, W.555 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.229, A:A.201 Hydrogen bonds: C:F.233, C:N.241, C:W.555

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ghosh, D., Structure of human placental steroid sulfatase at 2.0 angstrom resolution: Catalysis, quaternary association, and a secondary ligand site. J.Steroid Biochem.Mol.Biol. (2022)

Release Date

2022-12-07

Peptides

Steryl-sulfatase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Steryl-sulfatase