SMTL ID : 3pxo.1

Crystal structure of Metarhodopsin II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 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

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: T.4, N.15, G.18, V.20, R.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.7: 5 residues within 4Å: Chain B: T.4, N.15, G.18, V.20, R.21 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: N.2, S.281, D.282 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.2, S.281, D.282 No protein-ligand interaction detected (PLIP)

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

BOG.3: 7 residues within 4Å: Chain A: F.220, G.224, V.227, K.231, T.251, I.255, V.258 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.220, A:V.227, A:I.255, A:V.258 Hydrogen bonds: A:K.231 Salt bridges: A:K.231 BOG.4: 5 residues within 4Å: Chain A: Y.96, L.99, H.100, Y.102 Chain B: W.35 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.96, A:L.99, B:W.35, B:W.35, B:W.35, B:W.35 Hydrogen bonds: A:Y.102 Salt bridges: A:H.100 BOG.9: 7 residues within 4Å: Chain B: F.220, G.224, V.227, K.231, T.251, I.255, V.258 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.220, B:V.227, B:I.255, B:V.258 Hydrogen bonds: B:K.231 Salt bridges: B:K.231 BOG.10: 5 residues within 4Å: Chain A: W.35 Chain B: Y.96, L.99, H.100, Y.102 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.96, B:L.99, A:W.35, A:W.35, A:W.35, A:W.35 Hydrogen bonds: B:Y.102, B:Y.102 Salt bridges: B:H.100

2 x PLM: PALMITIC ACID(Covalent)

PLM.5: 6 residues within 4Å: Chain A: L.321, C.322, C.323 Chain B: R.252, Y.301, V.304 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.301 Hydrogen bonds: B:R.252 PLM.11: 6 residues within 4Å: Chain A: R.252, Y.301, V.304 Chain B: L.321, C.322, C.323 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.301 Hydrogen bonds: A:R.252

2 x RET: RETINAL(Covalent)

RET.6: 11 residues within 4Å: Chain A: M.86, A.117, E.122, M.207, H.211, F.212, W.265, Y.268, A.269, A.272, K.296 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.117, A:E.122, A:H.211, A:F.212, A:W.265, A:W.265, A:Y.268, A:Y.268, A:A.269, A:A.272, A:K.296 RET.12: 11 residues within 4Å: Chain B: M.86, A.117, E.122, M.207, H.211, F.212, W.265, Y.268, A.269, A.272, K.296 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.117, B:E.122, B:H.211, B:F.212, B:W.265, B:W.265, B:Y.268, B:Y.268, B:A.269, B:A.272, B:K.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choe, H.W. et al., Crystal structure of metarhodopsin II. Nature (2011)

Release Date

2011-03-09

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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