SMTL ID : 6eid.2 (1 other biounit)

Crystal structure of wild-type Channelrhodopsin 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

10 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.1: 4 residues within 4Å: Chain A: K.174, F.178, G.236, F.237 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.174, A:F.178, A:F.237, A:F.237 OLC.2: 7 residues within 4Å: Chain A: T.45, A.48, L.240, S.241, G.244, G.248 Ligands: OLC.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.45, A:T.45, A:S.241, A:S.241 OLC.3: 12 residues within 4Å: Chain A: F.100, K.103, N.104, P.105, S.106, L.119, A.122, L.126 Chain B: W.162, T.165, V.173, F.177 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.105, A:A.122, A:L.126, B:W.162, B:W.162, B:T.165, B:F.177 OLC.4: 7 residues within 4Å: Chain A: T.45, N.46, G.47, A.48, A.51, V.247 Ligands: OLC.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.51, A:V.247 Hydrogen bonds: A:T.45, A:N.46, A:G.47 OLC.5: 1 residues within 4Å: Chain A: W.217 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.217, A:W.217 OLC.8: 4 residues within 4Å: Chain B: K.174, F.178, G.236, F.237 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.174, B:F.178, B:F.237, B:F.237 OLC.9: 7 residues within 4Å: Chain B: T.45, A.48, L.240, S.241, G.244, G.248 Ligands: OLC.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.45, B:T.45, B:S.241, B:S.241 OLC.10: 12 residues within 4Å: Chain A: W.162, T.165, V.173, F.177 Chain B: F.100, K.103, N.104, P.105, S.106, L.119, A.122, L.126 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.162, A:W.162, A:T.165, A:F.177, B:P.105, B:A.122, B:L.126 OLC.11: 7 residues within 4Å: Chain B: T.45, N.46, G.47, A.48, A.51, V.247 Ligands: OLC.9 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.51, B:V.247 Hydrogen bonds: B:N.46, B:G.47 OLC.12: 1 residues within 4Å: Chain B: W.217 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.217, B:W.217

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 4 residues within 4Å: Chain A: R.148, F.190, H.191, K.194 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.148, A:H.191, A:K.194 PO4.7: 3 residues within 4Å: Chain A: H.201, K.205, R.209 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.201, A:K.205, A:R.209 PO4.13: 4 residues within 4Å: Chain B: R.148, F.190, H.191, K.194 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.148, B:H.191, B:K.194 PO4.14: 3 residues within 4Å: Chain B: H.201, K.205, R.209 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.201, B:K.205, B:R.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volkov, O. et al., Structural insights into ion conduction by channelrhodopsin 2. Science (2017)

Release Date

2017-12-06

Peptides

Archaeal-type opsin 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Membrane

We predict this structure to be a membrane protein.
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Archaeal-type opsin 2

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