SMTL ID : 5dys.1

Crystal Structure of T94I rhodopsin mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- BMA: alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-BMA.1: 6 residues within 4Å: Chain A: T.5, F.10, N.16, G.19, V.21, R.22 No protein-ligand interaction detected (PLIP)

1 x RET: RETINAL(Covalent)

RET.2: 11 residues within 4Å: Chain A: M.87, A.118, E.123, M.208, F.209, H.212, W.266, Y.269, A.270, A.273, K.297 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.123, A:H.212, A:W.266, A:W.266, A:Y.269, A:A.270, A:A.273, A:K.297

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: V.205, I.206, F.209, F.274, F.277 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.274, A:F.277 ACT.4: 4 residues within 4Å: Chain A: P.72, R.148, G.150, E.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.151 Salt bridges: A:R.148

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

BOG.5: 7 residues within 4Å: Chain A: F.221, G.225, K.232, E.248, K.249, T.252, V.255 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.221, A:V.255 Hydrogen bonds: A:K.232 Salt bridges: A:K.232 BOG.8: 5 residues within 4Å: Chain A: P.28, Y.30, Y.97, L.100, H.101 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.97 Hydrogen bonds: A:H.101 Salt bridges: A:H.101

2 x PLM: PALMITIC ACID(Covalent)

PLM.6: 3 residues within 4Å: Chain A: L.322, C.323 Ligands: PLM.7 No protein-ligand interaction detected (PLIP) PLM.7: 4 residues within 4Å: Chain A: L.322, C.323, C.324 Ligands: PLM.6 No protein-ligand interaction detected (PLIP)

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

SO4.9: 4 residues within 4Å: Chain A: G.285, P.286, I.287, F.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.285, A:I.287, A:F.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singhal, A. et al., Structural role of the T94I rhodopsin mutation in congenital stationary night blindness. Embo Rep. (2016)

Release Date

2016-08-10

Peptides

Rhodopsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Rhodopsin

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