SMTL ID : 4bez.1

Night blindness causing G90D rhodopsin in the active conformation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

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

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

ACT.2: 6 residues within 4Å: Chain A: V.205, I.206, F.209, A.273, F.274, F.277 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.206 ACT.7: 6 residues within 4Å: Chain B: V.205, I.206, F.209, A.273, F.274, F.277 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.206

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

SO4.3: 1 residues within 4Å: Chain A: E.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.151 SO4.8: 1 residues within 4Å: Chain B: E.151 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.75

2 x PLM: PALMITIC ACID(Covalent)

PLM.4: 9 residues within 4Å: Chain A: L.322, C.323, C.324 Chain B: I.257, T.298, V.301, Y.302, V.305, I.306 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.257, B:T.298, B:V.301, B:Y.302, B:V.305, B:I.306 PLM.9: 9 residues within 4Å: Chain A: I.257, T.298, V.301, Y.302, V.305, I.306 Chain B: L.322, C.323, C.324 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.257, A:T.298, A:V.301, A:Y.302, A:V.305, A:I.306

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

BOG.5: 8 residues within 4Å: Chain A: P.28, Y.30, Y.97, L.100, H.101 Chain B: E.34, W.36, M.40 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:W.36, B:W.36, B:W.36, A:Y.97, A:Y.97, A:L.100, A:L.100 Hydrogen bonds: A:Y.30, A:H.101 Salt bridges: A:H.101 BOG.10: 8 residues within 4Å: Chain A: E.34, W.36, M.40 Chain B: P.28, Y.30, Y.97, L.100, H.101 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:W.36, A:W.36, A:W.36, B:Y.97, B:Y.97, B:L.100, B:L.100 Hydrogen bonds: B:H.101 Salt bridges: B:H.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singhal, A. et al., Insights Into Congenital Stationary Night Blindness Based on the Structure of G90D Rhodopsin. Embo Rep. (2013)

Release Date

2013-04-24

Peptides

RHODOPSIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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RHODOPSIN

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