SMTL ID : 6is6.1

Crystal structure of Thermoplasmatales archaeon heliorhodopsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

OLC.1: 9 residues within 4Å: Chain A: V.33, L.37, S.70, I.71, E.72, P.75, L.76, M.79, F.82 Ligand excluded by PLIP OLC.2: 7 residues within 4Å: Chain A: S.245, W.249, F.252, A.253, R.257 Ligands: OLC.14, OLC.15 Ligand excluded by PLIP OLC.3: 13 residues within 4Å: Chain A: Y.170, G.177, F.178, W.181, F.185, A.206, F.209, N.210, A.213, I.214 Ligands: OLC.8, OLC.11, RET.13 Ligand excluded by PLIP OLC.4: 9 residues within 4Å: Chain A: M.79, F.82, T.86, A.87, L.95, Y.110, F.113, E.114 Ligands: OLC.7 Ligand excluded by PLIP OLC.5: 8 residues within 4Å: Chain A: F.208, C.211, K.225, H.231, K.234, I.238, L.239, V.242 Ligand excluded by PLIP OLC.6: 11 residues within 4Å: Chain A: R.98, Q.101, N.102, N.105, Y.110, F.113 Chain B: N.166, W.167, T.168, I.171 Ligands: OLC.23 Ligand excluded by PLIP OLC.7: 8 residues within 4Å: Chain A: I.71, L.76, I.117, L.135, L.138, L.139, F.142 Ligands: OLC.4 Ligand excluded by PLIP OLC.8: 12 residues within 4Å: Chain A: W.167, Y.170, I.171, C.174, I.175, F.178, V.179, Y.217, K.221 Ligands: OLC.3, OLC.21, OLC.27 Ligand excluded by PLIP OLC.9: 8 residues within 4Å: Chain A: F.197, Y.200, I.203, S.204, I.207, Q.250, A.253, G.254 Ligand excluded by PLIP OLC.10: 6 residues within 4Å: Chain A: R.16, K.17, I.20, I.24, I.31 Ligands: OLC.14 Ligand excluded by PLIP OLC.11: 9 residues within 4Å: Chain A: F.185, L.188, I.189, A.191, V.194, I.199, F.202, N.210 Ligands: OLC.3 Ligand excluded by PLIP OLC.12: 8 residues within 4Å: Chain A: V.49, K.51, E.66, L.68, L.135 Chain B: I.182, S.190 Ligands: OLC.23 Ligand excluded by PLIP OLC.14: 5 residues within 4Å: Chain A: I.28, I.31 Ligands: OLC.2, OLC.10, OLC.15 Ligand excluded by PLIP OLC.15: 7 residues within 4Å: Chain A: L.35, L.39, W.249, F.252, R.257 Ligands: OLC.2, OLC.14 Ligand excluded by PLIP OLC.16: 9 residues within 4Å: Chain B: V.33, L.37, S.70, I.71, E.72, P.75, L.76, M.79, F.82 Ligand excluded by PLIP OLC.17: 7 residues within 4Å: Chain B: S.245, W.249, F.252, A.253, R.257 Ligands: OLC.29, OLC.30 Ligand excluded by PLIP OLC.18: 13 residues within 4Å: Chain B: Y.170, G.177, F.178, W.181, F.185, A.206, F.209, N.210, A.213, I.214 Ligands: OLC.23, OLC.26, RET.28 Ligand excluded by PLIP OLC.19: 9 residues within 4Å: Chain B: M.79, F.82, T.86, A.87, L.95, Y.110, F.113, E.114 Ligands: OLC.22 Ligand excluded by PLIP OLC.20: 8 residues within 4Å: Chain B: F.208, C.211, K.225, H.231, K.234, I.238, L.239, V.242 Ligand excluded by PLIP OLC.21: 11 residues within 4Å: Chain A: N.166, W.167, T.168, I.171 Chain B: R.98, Q.101, N.102, N.105, Y.110, F.113 Ligands: OLC.8 Ligand excluded by PLIP OLC.22: 8 residues within 4Å: Chain B: I.71, L.76, I.117, L.135, L.138, L.139, F.142 Ligands: OLC.19 Ligand excluded by PLIP OLC.23: 12 residues within 4Å: Chain B: W.167, Y.170, I.171, C.174, I.175, F.178, V.179, Y.217, K.221 Ligands: OLC.6, OLC.12, OLC.18 Ligand excluded by PLIP OLC.24: 8 residues within 4Å: Chain B: F.197, Y.200, I.203, S.204, I.207, Q.250, A.253, G.254 Ligand excluded by PLIP OLC.25: 6 residues within 4Å: Chain B: R.16, K.17, I.20, I.24, I.31 Ligands: OLC.29 Ligand excluded by PLIP OLC.26: 9 residues within 4Å: Chain B: F.185, L.188, I.189, A.191, V.194, I.199, F.202, N.210 Ligands: OLC.18 Ligand excluded by PLIP OLC.27: 8 residues within 4Å: Chain A: I.182, S.190 Chain B: V.49, K.51, E.66, L.68, L.135 Ligands: OLC.8 Ligand excluded by PLIP OLC.29: 5 residues within 4Å: Chain B: I.28, I.31 Ligands: OLC.17, OLC.25, OLC.30 Ligand excluded by PLIP OLC.30: 7 residues within 4Å: Chain B: L.35, L.39, W.249, F.252, R.257 Ligands: OLC.17, OLC.29 Ligand excluded by PLIP

2 x RET: RETINAL(Covalent)

RET.13: 18 residues within 4Å: Chain A: W.112, Y.115, S.118, A.119, M.122, M.148, N.149, G.152, Y.170, G.173, C.174, F.209, F.212, A.213, M.216, S.240, K.244 Ligands: OLC.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.112, A:W.112, A:Y.115, A:Y.115, A:A.119, A:Y.170, A:F.209, A:F.209, A:F.212, A:F.212, A:F.212, A:A.213, A:M.216, A:K.244 RET.28: 18 residues within 4Å: Chain B: W.112, Y.115, S.118, A.119, M.122, M.148, N.149, G.152, Y.170, G.173, C.174, F.209, F.212, A.213, M.216, S.240, K.244 Ligands: OLC.18 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.112, B:W.112, B:Y.115, B:Y.115, B:A.119, B:Y.170, B:F.209, B:F.209, B:F.212, B:F.212, B:F.212, B:A.213, B:M.216, B:K.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shihoya, W. et al., Crystal structure of heliorhodopsin. Nature (2019)

Release Date

2019-09-25

Peptides

heliorhodopsin: 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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heliorhodopsin

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