SMTL ID : 5wkt.1

3.2-Angstrom In situ Mylar structure of bovine opsin at 100 K

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 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

NAG-NAG-BMA-MAN.1: 6 residues within 4Å: Chain A: T.4, F.9, N.15, G.18, V.20, R.21 No protein-ligand interaction detected (PLIP)

1 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.2: 4 residues within 4Å: Chain A: K.66, R.69, Y.74, E.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.66, A:K.66, A:R.69 Salt bridges: A:R.69

3 x BOG: octyl beta-D-glucopyranoside(Post Translational Modification)(Non-covalent)

BOG.3: 18 residues within 4Å: Chain A: G.114, A.117, T.118, G.121, E.122, Y.178, C.187, G.188, I.189, Y.191, V.204, M.207, F.208, F.212, W.265, Y.268, A.269, A.272 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.207, A:Y.268, A:Y.268 Hydrogen bonds: A:C.187, A:Y.268 BOG.4: 10 residues within 4Å: Chain A: F.220, Y.223, G.224, V.227, K.231, E.247, T.251, V.254, I.255, V.258 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.220, A:T.251, A:V.254, A:I.255 Hydrogen bonds: A:K.231, A:T.251 Salt bridges: A:K.231 BOG.5: 7 residues within 4Å: Chain A: P.27, Y.29, Y.96, L.99, H.100, G.101, Y.102 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.96, A:Y.96, A:L.99 Hydrogen bonds: A:Y.29, A:Y.29 Salt bridges: A:H.100

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

SO4.6: 3 residues within 4Å: Chain B: I.1, L.2, E.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.1, B:I.1, B:L.2, B:E.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Broecker, J. et al., High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions. Nat Protoc (2018)

Release Date

2017-12-13

Peptides

Rhodopsin: A
Transducin Galpha peptide: B

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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Rhodopsin

Transducin Galpha peptide

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