SMTL ID : 7d7q.1

Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta rhodopsin phosphodiesterase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-dimer

Ligands

2 x RET: RETINAL(Covalent)

RET.1: 15 residues within 4Å: Chain A: Y.131, W.134, T.137, C.138, L.166, L.167, G.170, F.185, 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:T.137, A:L.166, A:F.185, A:Y.192, A:W.233, A:W.233, A:F.236, A:F.236, A:F.236, A:P.237, A:E.240, A:K.265 RET.5: 15 residues within 4Å: Chain B: Y.131, W.134, C.138, L.166, L.167, G.170, F.185, S.188, Y.192, W.233, F.236, P.237, E.240, D.261, K.265 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.131, B:W.134, B:W.134, B:W.134, B:L.166, B:F.185, B:Y.192, B:Y.192, B:W.233, B:W.233, B:F.236, B:F.236, B:P.237, B:E.240, B:K.265

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

OLC.2: 7 residues within 4Å: Chain A: F.61, T.65, A.255, V.259, Y.262 Chain B: A.64, V.67 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.64, B:V.67, A:V.259, A:Y.262 OLC.3: 11 residues within 4Å: Chain A: F.27, V.31, I.135, I.136, T.140, Y.143, V.156, S.157, A.160, T.161, A.164 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.27, A:F.27, A:Y.143, A:A.160, A:A.164 OLC.4: 5 residues within 4Å: Chain A: F.189, M.196, L.197, L.238, F.241 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.189, A:L.197 OLC.6: 8 residues within 4Å: Chain B: V.35, A.132, I.135, P.139, A.160, T.161, A.164, L.172 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.35, B:A.132, B:I.135, B:I.135, B:A.164, B:L.172

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
B

Membrane

We predict this structure to be a membrane protein.
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Phosphodiesterase