SMTL ID : 7d7p.1

Crystal structure of the phosphodiesterase domain of Salpingoeca rosetta rhodopsin phosphodiesterase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.1: 10 residues within 4Å: Chain A: K.35, G.36, S.38, A.40, Q.82, F.83, N.84, E.133, N.197, E.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.35, A:N.84 2PE.8: 10 residues within 4Å: Chain B: K.35, G.36, S.38, A.40, Q.82, F.83, N.84, E.133, N.197, E.202 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.35, B:N.84

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

PEG.2: 8 residues within 4Å: Chain A: N.155, I.159, D.171, Q.172, S.173, V.174, D.218, A.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.173, A:V.174 Water bridges: A:A.220 PEG.9: 8 residues within 4Å: Chain B: N.155, I.159, D.171, Q.172, S.173, V.174, D.218, A.220 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.173, B:V.174 Water bridges: B:A.220

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

EDO.3: 3 residues within 4Å: Chain A: K.61, V.69, R.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.61 EDO.4: 2 residues within 4Å: Chain A: R.277, K.280 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.280 EDO.5: 6 residues within 4Å: Chain A: H.150, N.151, G.152, L.153, H.158, L.175 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.151, A:N.151, A:L.153, A:L.153 Water bridges: A:D.149 EDO.10: 3 residues within 4Å: Chain B: K.61, V.69, R.72 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.61 EDO.11: 2 residues within 4Å: Chain B: R.277, K.280 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.280 EDO.12: 6 residues within 4Å: Chain B: H.150, N.151, G.152, L.153, H.158, L.175 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.151, B:N.151, B:L.153, B:L.153 Water bridges: B:D.149

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: H.111, H.146, D.147, D.260 Ligands: MG.7 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.111, A:H.146, A:D.147, A:D.260, H2O.1, H2O.3 ZN.13: 5 residues within 4Å: Chain B: H.111, H.146, D.147, D.260 Ligands: MG.14 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.111, B:H.146, B:D.147, B:D.260, H2O.8, H2O.10

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain A: D.147 Ligands: ZN.6 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.147, H2O.1, H2O.1, H2O.3, H2O.3, H2O.4 MG.14: 2 residues within 4Å: Chain B: D.147 Ligands: ZN.13 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.147, H2O.8, H2O.8, H2O.9, H2O.9, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ikuta, T. et al., Structural insights into the mechanism of rhodopsin phosphodiesterase. Nat Commun (2020)

Release Date

2020-11-18

Peptides

Phosphodiesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Phosphodiesterase