SMTL ID : 6y0k.1

Sulfite oxidase from Thermus thermophilus with coordinated phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x MSS: (MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM(Non-covalent)

MSS.1: 21 residues within 4Å: Chain A: Y.48, I.49, R.50, N.51, N.52, V.53, L.100, C.102, S.103, A.156, F.165, H.192, R.197, G.205, V.206, N.208, V.209, K.210, W.211, Y.231 Ligands: PO4.8 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Y.48, A:R.50, A:R.50, A:R.50, A:N.52, A:N.52, A:V.53, A:V.53, A:S.103, A:R.197, A:V.206, A:N.208, A:K.210, A:K.210 Salt bridges: A:H.192, A:R.197, A:K.210 pi-Stacking: A:F.165 MSS.10: 21 residues within 4Å: Chain B: Y.48, I.49, R.50, N.51, N.52, V.53, L.100, C.102, S.103, A.156, F.165, H.192, R.197, G.205, V.206, N.208, V.209, K.210, W.211, Y.231 Ligands: PO4.17 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Y.48, B:R.50, B:R.50, B:R.50, B:N.52, B:N.52, B:V.53, B:V.53, B:S.103, B:R.197, B:V.206, B:N.208, B:K.210, B:K.210 Salt bridges: B:H.192, B:R.197, B:K.210 pi-Stacking: B:F.165

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: H.155, K.214, E.216 Ligands: PO4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.155 Water bridges: A:F.217 GOL.3: 6 residues within 4Å: Chain A: V.96, R.133, H.176, P.201, F.324 Ligands: PO4.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.133, A:H.176 Water bridges: A:R.133 GOL.4: 2 residues within 4Å: Chain A: R.286, E.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.328 Water bridges: A:E.288, A:E.288, A:R.328 GOL.9: 2 residues within 4Å: Chain A: H.172 Chain B: L.244 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:H.172, B:Q.246, B:Q.246 GOL.11: 4 residues within 4Å: Chain B: H.155, K.214, E.216 Ligands: PO4.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.155, B:E.216 Water bridges: B:F.217 GOL.12: 6 residues within 4Å: Chain B: V.96, R.133, H.176, P.201, F.324 Ligands: PO4.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.133 Water bridges: B:R.133 GOL.13: 2 residues within 4Å: Chain B: R.286, E.288 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.328 Water bridges: B:E.288, B:E.288, B:R.328 GOL.18: 2 residues within 4Å: Chain A: L.244 Chain B: H.172 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:H.172, A:Q.246, A:Q.246

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

PO4.5: 6 residues within 4Å: Chain A: H.155, R.158, E.164, V.166, K.214 Ligands: PO4.6 7 PLIP interactions: 7 interactions with chain A Water bridges: A:A.156, A:R.158, A:R.158, A:K.214 Salt bridges: A:H.155, A:R.158, A:K.214 PO4.6: 7 residues within 4Å: Chain A: T.153, H.155, V.166, N.222, T.224 Ligands: GOL.2, PO4.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.223, A:T.223 Salt bridges: A:H.155 PO4.7: 6 residues within 4Å: Chain A: V.96, T.97, S.323, F.324, G.325 Ligands: GOL.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.97, A:S.323, A:F.324, A:G.325 Water bridges: A:T.97, A:T.97, A:S.323 PO4.8: 9 residues within 4Å: Chain A: R.50, C.102, G.104, R.107, N.117, W.119, Y.231, Y.367 Ligands: MSS.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.104, A:N.117, A:Y.231, A:Y.231 Water bridges: A:N.117, A:R.230 Salt bridges: A:R.50, A:R.107 PO4.14: 6 residues within 4Å: Chain B: H.155, R.158, E.164, V.166, K.214 Ligands: PO4.15 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.164 Water bridges: B:H.155, B:A.156, B:R.158, B:R.158, B:K.214 Salt bridges: B:H.155, B:R.158, B:K.214 PO4.15: 7 residues within 4Å: Chain B: T.153, H.155, V.166, N.222, T.224 Ligands: GOL.11, PO4.14 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.223, B:T.223 Salt bridges: B:H.155 PO4.16: 6 residues within 4Å: Chain B: V.96, T.97, S.323, F.324, G.325 Ligands: GOL.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.97, B:S.323, B:F.324, B:G.325 Water bridges: B:T.97, B:S.323 PO4.17: 9 residues within 4Å: Chain B: R.50, C.102, G.104, R.107, N.117, W.119, Y.231, Y.367 Ligands: MSS.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.104, B:N.117, B:Y.231, B:Y.231 Water bridges: B:N.117, B:R.230, B:Y.367 Salt bridges: B:R.50, B:R.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Djeghader, A. et al., Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase. Chem.Commun.(Camb.) (2020)

Release Date

2020-08-05

Peptides

Putaitve sulfite oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Putaitve sulfite oxidase