SMTL ID : 3ug9.1

Crystal Structure of the Closed State of Channelrhodopsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x RET: RETINAL(Covalent)

RET.1: 15 residues within 4Å: Chain A: W.140, T.143, C.144, T.175, G.179, F.194, G.197, L.198, W.239, F.242, P.243, F.246, D.269, S.272, K.273 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.140, A:W.140, A:F.194, A:F.194, A:W.239, A:W.239, A:F.242, A:F.242, A:F.242, A:F.242, A:P.243, A:P.243, A:K.273 RET.8: 15 residues within 4Å: Chain B: W.140, T.143, C.144, T.175, G.179, F.194, G.197, L.198, W.239, F.242, P.243, F.246, D.269, S.272, K.273 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.140, B:W.140, B:F.194, B:F.194, B:W.239, B:W.239, B:F.242, B:F.242, B:F.242, B:F.242, B:P.243, B:P.243, B:K.273

12 x OLA: OLEIC ACID(Non-covalent)(Non-functional Binders)

OLA.2: 8 residues within 4Å: Chain A: K.163, G.167, V.170, S.171, C.199, Y.200, Y.203 Chain B: W.97 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.170, A:Y.200, A:Y.200, A:Y.200, B:W.97 Hydrogen bonds: A:K.163, A:G.167 OLA.3: 13 residues within 4Å: Chain A: I.112, H.116, D.119, E.120, P.121, A.122, L.135, A.138, L.142 Chain B: T.181, V.189, F.193 Ligands: OLA.11 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.112, A:I.112, A:H.116, A:D.119, A:P.121, A:A.122, A:L.135, A:A.138, A:L.142, B:V.189, B:F.193 Salt bridges: A:H.116 OLA.4: 5 residues within 4Å: Chain A: I.192, F.193, M.196 Chain B: H.116 Ligands: OLA.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.192, A:F.193, A:F.193 OLA.5: 8 residues within 4Å: Chain A: K.186, G.187, R.190, V.191, F.194, L.195, G.252, F.253 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.190, A:V.191, A:F.194, A:F.194, A:L.195, A:F.253, A:F.253 Hydrogen bonds: A:G.187 Salt bridges: A:R.190 OLA.6: 7 residues within 4Å: Chain A: E.64, M.241, L.256, G.260, G.264, I.267, I.268 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.256, A:I.267, A:I.268 OLA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) OLA.9: 8 residues within 4Å: Chain A: W.97 Chain B: K.163, G.167, V.170, S.171, C.199, Y.200, Y.203 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:W.97, B:V.170, B:Y.200, B:Y.200, B:Y.200 Hydrogen bonds: B:K.163, B:G.167 OLA.10: 13 residues within 4Å: Chain A: T.181, V.189, F.193 Chain B: I.112, H.116, D.119, E.120, P.121, A.122, L.135, A.138, L.142 Ligands: OLA.4 12 PLIP interactions: 2 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:V.189, A:F.193, B:I.112, B:I.112, B:H.116, B:D.119, B:P.121, B:A.122, B:L.135, B:A.138, B:L.142 Salt bridges: B:H.116 OLA.11: 5 residues within 4Å: Chain A: H.116 Chain B: I.192, F.193, M.196 Ligands: OLA.3 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.192, B:F.193, B:F.193 OLA.12: 8 residues within 4Å: Chain B: K.186, G.187, R.190, V.191, F.194, L.195, G.252, F.253 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:R.190, B:V.191, B:F.194, B:F.194, B:L.195, B:F.253, B:F.253 Hydrogen bonds: B:G.187 Salt bridges: B:R.190 OLA.13: 7 residues within 4Å: Chain B: E.64, M.241, L.256, G.260, G.264, I.267, I.268 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.256, B:I.267, B:I.268 OLA.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kato, H.E. et al., Crystal structure of the channelrhodopsin light-gated cation channel. Nature (2012)

Release Date

2012-01-25

Peptides

Archaeal-type opsin 1, Archaeal-type opsin 2: 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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Archaeal-type opsin 1, Archaeal-type opsin 2