SMTL ID : 3qap.1

Crystal structure of Natronomonas pharaonis sensory rhodopsin II in the ground state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: W.76, T.80, V.108, M.109, G.112, F.127, G.130, A.131, F.134, W.171, Y.174, P.175, W.178, D.201, T.204, K.205 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.76, A:W.76, A:W.76, A:T.80, A:V.108, A:F.127, A:F.127, A:F.134, A:W.171, A:W.171, A:Y.174, A:Y.174, A:Y.174, A:Y.174, A:P.175, A:P.175, A:W.178, A:W.178, A:K.205

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

BOG.2: 4 residues within 4Å: Chain A: L.104, V.132, G.136, Y.139 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.104, A:Y.139 Water bridges: A:Y.140, A:Y.140

29 x LFA: EICOSANE(Non-covalent)(Non-functional Binders)

LFA.3: 8 residues within 4Å: Chain A: E.33, Y.36, Y.37, L.40, I.156, A.212, L.213, A.216 Ligand excluded by PLIP LFA.4: 5 residues within 4Å: Chain A: F.113, A.114, M.117 Ligands: LFA.8, L2P.18 Ligand excluded by PLIP LFA.5: 4 residues within 4Å: Chain A: V.53 Ligands: L2P.18, LFA.27, LFA.33 Ligand excluded by PLIP LFA.6: 3 residues within 4Å: Chain A: I.77, T.106 Ligands: L2P.18 Ligand excluded by PLIP LFA.7: 4 residues within 4Å: Chain A: V.138, Y.139, V.142, G.143 Ligand excluded by PLIP LFA.8: 3 residues within 4Å: Chain A: A.114, M.117 Ligands: LFA.4 Ligand excluded by PLIP LFA.9: 5 residues within 4Å: Chain A: R.35, T.39, G.42, L.82 Ligands: LFA.25 Ligand excluded by PLIP LFA.10: 2 residues within 4Å: Chain A: I.173 Ligands: LFA.12 Ligand excluded by PLIP LFA.11: 1 residues within 4Å: Chain A: W.24 Ligand excluded by PLIP LFA.12: 4 residues within 4Å: Chain A: F.176, L.187 Ligands: LFA.10, LFA.32 Ligand excluded by PLIP LFA.13: 7 residues within 4Å: Chain A: W.9, L.16, V.52, L.56 Ligands: LFA.19, LFA.22, LFA.27 Ligand excluded by PLIP LFA.14: 6 residues within 4Å: Chain A: T.5, W.9, A.55, L.56, G.57 Ligands: LFA.22 Ligand excluded by PLIP LFA.15: 6 residues within 4Å: Chain A: I.121, Y.124, A.125, G.128, V.132 Ligands: L2P.21 Ligand excluded by PLIP LFA.16: 7 residues within 4Å: Chain A: Y.199, V.203, G.207, F.210, I.211, D.214 Ligands: LFA.28 Ligand excluded by PLIP LFA.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LFA.19: 7 residues within 4Å: Chain A: L.16, T.19, G.45, V.49 Ligands: LFA.13, L2P.18, LFA.27 Ligand excluded by PLIP LFA.20: 3 residues within 4Å: Chain A: T.6, W.9 Ligands: LFA.22 Ligand excluded by PLIP LFA.22: 5 residues within 4Å: Chain A: W.9, I.13 Ligands: LFA.13, LFA.14, LFA.20 Ligand excluded by PLIP LFA.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LFA.24: 3 residues within 4Å: Chain A: L.82, Y.85 Ligands: LFA.26 Ligand excluded by PLIP LFA.25: 6 residues within 4Å: Chain A: A.23, G.26, V.41, G.42 Ligands: LFA.9, L2P.18 Ligand excluded by PLIP LFA.26: 3 residues within 4Å: Chain A: L.93, F.98 Ligands: LFA.24 Ligand excluded by PLIP LFA.27: 7 residues within 4Å: Chain A: V.52, L.56, V.58 Ligands: LFA.5, LFA.13, LFA.19, LFA.33 Ligand excluded by PLIP LFA.28: 9 residues within 4Å: Chain A: L.7, L.10, G.14, A.195, V.198, Y.199, L.202 Ligands: LFA.16, LFA.29 Ligand excluded by PLIP LFA.29: 5 residues within 4Å: Chain A: G.3, T.6, L.7 Ligands: LFA.28, LFA.30 Ligand excluded by PLIP LFA.30: 1 residues within 4Å: Ligands: LFA.29 Ligand excluded by PLIP LFA.31: 2 residues within 4Å: Chain A: S.95, R.96 Ligand excluded by PLIP LFA.32: 5 residues within 4Å: Chain A: F.176, L.180, V.185, L.187 Ligands: LFA.12 Ligand excluded by PLIP LFA.33: 4 residues within 4Å: Chain A: V.58 Ligands: LFA.5, L2P.18, LFA.27 Ligand excluded by PLIP

2 x L2P: 2,3-DI-PHYTANYL-GLYCEROL(Non-covalent)

L2P.18: 19 residues within 4Å: Chain A: G.45, I.46, V.49, A.50, V.58, G.59, V.61, P.71, I.74, D.75, I.77, L.78, F.113 Ligands: LFA.4, LFA.5, LFA.6, LFA.19, LFA.25, LFA.33 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.46, A:V.49, A:A.50, A:P.71, A:P.71, A:I.74, A:I.77, A:L.78, A:L.78, A:F.113, A:F.113 Hydrogen bonds: A:G.59 L2P.21: 8 residues within 4Å: Chain A: A.131, F.134, L.135, V.168, P.175, F.176, L.179 Ligands: LFA.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.134, A:F.134, A:V.168, A:F.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gushchin, I. et al., Active State of Sensory Rhodopsin II: Structural Determinants for Signal Transfer and Proton Pumping. J.Mol.Biol. (2011)

Release Date

2011-09-14

Peptides

Sensory rhodopsin-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Sensory rhodopsin-2

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