SMTL ID : 7cj3.1

Crystal structure of the transmembrane domain of Salpingoeca rosetta rhodopsin phosphodiesterase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x RET: RETINAL(Covalent)

RET.1: 18 residues within 4Å: Chain A: Y.131, W.134, T.137, C.138, L.141, L.166, L.167, G.170, F.185, S.188, F.189, Y.192, W.233, F.236, P.237, E.240, D.261, K.265 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.131, A:W.134, A:L.141, A:L.166, A:L.167, A:F.185, A:Y.192, A:Y.192, A:W.233, A:F.236, A:F.236, A:F.236, A:E.240, A:K.265 RET.9: 15 residues within 4Å: Chain B: Y.131, W.134, T.137, C.138, L.141, L.166, L.167, G.170, F.185, Y.192, W.233, F.236, P.237, D.261, K.265 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.131, B:W.134, B:W.134, B:L.141, B:L.166, B:L.167, B:F.185, B:Y.192, B:Y.192, B:W.233, B:F.236, B:F.236, B:F.236, B:P.237, B:K.265

14 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)(Non-functional Binders)

OLC.2: 12 residues within 4Å: Chain A: F.61, T.65, A.68, C.258, V.259, Y.262 Chain B: Q.59, S.60, G.63, A.64, V.67, A.68 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.61, A:A.68, A:V.259, A:Y.262, B:Q.59, B:A.64, B:V.67 OLC.3: 6 residues within 4Å: Chain A: V.35, S.38, F.42, Y.115, L.128, I.135 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.35, A:F.42, A:F.42, A:F.42, A:Y.115, A:L.128, A:I.135 OLC.4: 13 residues within 4Å: Chain A: S.178, A.181, F.182, F.185, F.189, I.193, V.230, P.237, L.238, F.241, R.244, Q.245 Ligands: OLC.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.182, A:F.185, A:F.185, A:F.189, A:I.193, A:V.230, A:L.238, A:F.241, A:F.241, A:F.241 Hydrogen bonds: A:A.181 OLC.5: 6 residues within 4Å: Chain A: W.200, G.204, M.207, Q.208, R.226 Ligands: OLC.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.200, A:W.200 Hydrogen bonds: A:R.226 Salt bridges: A:R.226 OLC.6: 4 residues within 4Å: Chain A: A.190, Y.194, L.197, H.198 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.190, A:Y.194, A:Y.194, A:L.197 OLC.7: 7 residues within 4Å: Chain A: Q.22, I.29, A.70, Y.80, A.96, Y.97, G.100 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.29, A:A.96, A:Y.97, A:Y.97 Hydrogen bonds: A:Q.22 OLC.8: 4 residues within 4Å: Chain A: F.41, F.42, A.43, N.44 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.41, A:F.41, A:F.42 Hydrogen bonds: A:N.44 OLC.10: 15 residues within 4Å: Chain A: S.56, Q.59, S.60, G.63, A.64, V.67, A.68 Chain B: H.57, F.61, T.65, A.68, A.255, C.258, V.259, Y.262 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.61, B:A.68, B:A.255, B:V.259, B:Y.262, A:V.67, A:V.67 Salt bridges: B:H.57 Hydrogen bonds: A:S.56, A:Q.59 Water bridges: A:Q.59 OLC.11: 4 residues within 4Å: Chain B: Y.115, L.128, I.135, A.171 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.115, B:L.128, B:I.135, B:A.171 OLC.12: 7 residues within 4Å: Chain B: I.193, L.197, W.200, G.204, Q.208, R.226, S.234 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.193, B:L.197, B:W.200 Hydrogen bonds: B:Q.208 Salt bridges: B:R.226 OLC.13: 4 residues within 4Å: Chain B: A.190, Y.194, L.197, H.198 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.190, B:Y.194, B:Y.194, B:L.197 OLC.14: 1 residues within 4Å: Ligands: OLC.16 No protein-ligand interaction detected (PLIP) OLC.15: 9 residues within 4Å: Chain B: T.18, K.19, Q.22, A.70, T.73, Y.80, A.96, Y.97, G.100 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.73, B:Y.80, B:A.96, B:Y.97, B:Y.97, B:Y.97 OLC.16: 4 residues within 4Å: Chain B: Q.24, F.27, T.140 Ligands: OLC.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.24, B:F.27, B:T.140

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

2020-11-25

Peptides

Phosphodiesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Phosphodiesterase