SMTL ID : 7z0d.1

Crystal structure of the L state of bacteriorhodopsin at 1.20 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

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

LFA.1: 4 residues within 4Å: Chain A: F.54, L.58, L.62 Ligands: LFA.7 Ligand excluded by PLIP LFA.2: 9 residues within 4Å: Chain A: L.146, L.149, Y.150, F.153, F.154, V.179 Ligands: LFA.5, LFA.18, LFA.27 Ligand excluded by PLIP LFA.4: 6 residues within 4Å: Chain A: I.198, V.199, P.200, I.203, L.207 Ligands: LFA.15 Ligand excluded by PLIP LFA.5: 3 residues within 4Å: Chain A: Y.150, F.154 Ligands: LFA.2 Ligand excluded by PLIP LFA.6: 6 residues within 4Å: Chain A: K.172, V.173, N.176, V.177, V.180 Ligands: LFA.13 Ligand excluded by PLIP LFA.7: 11 residues within 4Å: Chain A: W.10, A.14, T.17, A.18, G.21, L.22, L.25, F.54, L.61 Ligands: LFA.1, LFA.16 Ligand excluded by PLIP LFA.8: 6 residues within 4Å: Chain A: W.138, A.139, T.142, A.143, L.146 Ligands: OLA.25 Ligand excluded by PLIP LFA.9: 6 residues within 4Å: Chain A: S.132, F.135, V.136, A.139 Ligands: LFA.22, OLA.25 Ligand excluded by PLIP LFA.10: 8 residues within 4Å: Chain A: L.48, I.52, T.55, M.56, F.88, L.92 Ligands: LFA.12, OLC.23 Ligand excluded by PLIP LFA.12: 7 residues within 4Å: Chain A: L.87, F.88, P.91, L.92, L.95, V.112 Ligands: LFA.10 Ligand excluded by PLIP LFA.13: 5 residues within 4Å: Chain A: K.172, N.176, V.180 Ligands: LFA.6, LFA.26 Ligand excluded by PLIP LFA.14: 5 residues within 4Å: Chain A: V.180, S.183, A.184, V.187 Ligands: LFA.26 Ligand excluded by PLIP LFA.15: 4 residues within 4Å: Chain A: I.191, I.198, V.199 Ligands: LFA.4 Ligand excluded by PLIP LFA.16: 7 residues within 4Å: Chain A: W.10, I.11, A.14, L.15, A.18 Ligands: LFA.7, LFA.17 Ligand excluded by PLIP LFA.17: 5 residues within 4Å: Chain A: W.10, I.11, L.15, L.19 Ligands: LFA.16 Ligand excluded by PLIP LFA.18: 7 residues within 4Å: Chain A: A.143, L.146, Y.147, Y.150 Ligands: LFA.2, OLC.3, LFA.19 Ligand excluded by PLIP LFA.19: 4 residues within 4Å: Chain A: Y.147, Y.150 Ligands: OLC.3, LFA.18 Ligand excluded by PLIP LFA.20: 6 residues within 4Å: Chain A: L.19, M.209, V.210, V.213, S.214 Ligands: OLC.11 Ligand excluded by PLIP LFA.21: 8 residues within 4Å: Chain A: T.67, W.80, A.84, L.87, F.88, L.123, L.127 Ligands: OLC.23 Ligand excluded by PLIP LFA.22: 4 residues within 4Å: Chain A: S.132, Y.133, V.136 Ligands: LFA.9 Ligand excluded by PLIP LFA.24: 3 residues within 4Å: Chain A: L.25, Y.26, V.29 Ligand excluded by PLIP LFA.26: 6 residues within 4Å: Chain A: V.179, V.180, S.183 Ligands: LFA.13, LFA.14, LFA.27 Ligand excluded by PLIP LFA.27: 13 residues within 4Å: Chain A: W.138, T.142, M.145, L.146, L.149, V.179, S.183, P.186, V.187, L.190 Ligands: LFA.2, OLA.25, LFA.26 Ligand excluded by PLIP

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

OLC.3: 11 residues within 4Å: Chain A: G.106, T.107, A.110, A.114, I.117, I.140, A.143, A.144, Y.147 Ligands: LFA.18, LFA.19 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.110, A:A.114, A:I.117, A:I.140, A:A.144 Hydrogen bonds: A:T.107 Water bridges: A:T.107 OLC.11: 10 residues within 4Å: Chain A: L.19, L.22, G.23, Y.26, V.213, S.214, V.217, G.218, L.221 Ligands: LFA.20 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.19, A:V.213, A:V.217, A:L.221 Hydrogen bonds: A:Y.26 OLC.23: 7 residues within 4Å: Chain A: M.56, Y.64, W.80, A.84, F.88 Ligands: LFA.10, LFA.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.64 Water bridges: A:W.80

1 x OLA: OLEIC ACID(Non-covalent)

OLA.25: 8 residues within 4Å: Chain A: Y.131, F.135, W.138, L.190, A.196 Ligands: LFA.8, LFA.9, LFA.27 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.131, A:F.135, A:F.135, A:F.135, A:L.190, A:L.190, A:A.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borshchevskiy, V. et al., True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins. Nat.Struct.Mol.Biol. (2022)

Release Date

2022-05-04

Peptides

Bacteriorhodopsin: 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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Bacteriorhodopsin

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