SMTL ID : 4ww3.2 (1 other biounit)

Crystal structure of the lumi intermediate of squid rhodopsin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: S.140, R.142, R.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.140, A:S.140 Salt bridges: A:K.137, A:R.143

1 x RET: RETINAL(Covalent)

RET.2: 16 residues within 4Å: Chain A: N.79, Y.103, G.104, G.107, G.108, G.111, F.112, N.177, C.178, F.180, M.196, F.197, F.201, W.266, A.270, K.297 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.112, A:F.112, A:F.180, A:F.180, A:F.197, A:F.197, A:F.197, A:F.201, A:F.201, A:F.201, A:W.266, A:A.270, A:K.297

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.3: 5 residues within 4Å: Chain A: I.48, K.53, F.70, F.73, T.74 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.48, A:I.48, A:F.70, A:F.73, A:T.74 Hydrogen bonds: A:K.53 PLM.4: 9 residues within 4Å: Chain A: I.35, I.39, M.305, S.308, V.309, V.325, C.328, C.329 Ligands: TWT.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.35, A:I.39

1 x TWT: DOCOSANE(Non-covalent)

TWT.5: 5 residues within 4Å: Chain A: G.42, G.43, P.304, S.308 Ligands: PLM.4 No protein-ligand interaction detected (PLIP)

1 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.6: 5 residues within 4Å: Chain A: R.185, S.187, R.190, S.191, L.194 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.190, A:L.194 Salt bridges: A:R.190, A:R.190

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

BOG.7: 14 residues within 4Å: Chain A: T.59, A.61, N.62, I.65, I.121, R.125, K.138, E.248, L.251, I.254, S.255, K.313, D.339, E.343 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.61, A:I.65, A:I.121, A:L.251, A:I.254 Hydrogen bonds: A:T.59, A:K.313, A:D.339, A:E.343, A:E.343 Water bridges: A:M.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murakami, M. et al., Crystallographic Study of the LUMI Intermediate of Squid Rhodopsin. Plos One (2015)

Release Date

2015-06-17

Peptides

Rhodopsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

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