SMTL ID : 7z0e.1

Crystal structure of the M state of bacteriorhodopsin at 1.22 Angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

monomer

Ligands

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

OLC.1: 14 residues within 4Å: Chain A: G.21, T.24, L.25, L.28, K.40, Y.43, A.44, T.47, L.48, A.51, F.54, T.55 Ligands: LFA.2, LFA.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.25, A:L.28, A:T.47, A:L.48, A:F.54, A:F.54, A:F.54 Hydrogen bonds: A:K.40

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

LFA.2: 10 residues within 4Å: Chain A: A.14, T.17, A.18, G.21, L.22, L.25, F.54, L.61 Ligands: OLC.1, LFA.3 Ligand excluded by PLIP LFA.3: 6 residues within 4Å: Chain A: T.17, F.54, L.58, L.62 Ligands: OLC.1, LFA.2 Ligand excluded by PLIP LFA.4: 6 residues within 4Å: Chain A: W.10, I.11, L.15 Ligands: LFA.8, SQL.11, LFA.12 Ligand excluded by PLIP LFA.5: 8 residues within 4Å: Chain A: L.87, F.88, P.91, L.92, L.95, V.112, G.116 Ligands: L2P.9 Ligand excluded by PLIP LFA.6: 4 residues within 4Å: Chain A: V.173, I.222 Ligands: LFA.7, LFA.22 Ligand excluded by PLIP LFA.7: 9 residues within 4Å: Chain A: K.172, V.173, N.176, V.177, V.180, L.181 Ligands: LFA.6, LFA.17, LFA.22 Ligand excluded by PLIP LFA.8: 3 residues within 4Å: Chain A: I.11, W.12 Ligands: LFA.4 Ligand excluded by PLIP LFA.10: 5 residues within 4Å: Chain A: Y.131, S.132, F.135, V.136, A.139 Ligand excluded by PLIP LFA.12: 6 residues within 4Å: Chain A: W.10, I.11, A.14, L.15, A.18 Ligands: LFA.4 Ligand excluded by PLIP LFA.13: 2 residues within 4Å: Chain A: Y.147, Y.150 Ligand excluded by PLIP LFA.14: 4 residues within 4Å: Chain A: I.191, I.198, V.199 Ligands: LFA.19 Ligand excluded by PLIP LFA.15: 14 residues within 4Å: Chain A: W.138, T.142, M.145, L.146, L.149, Y.150, F.153, F.154, V.179, S.183, P.186, V.187, L.190 Ligands: LFA.18 Ligand excluded by PLIP LFA.16: 3 residues within 4Å: Chain A: L.25, Y.26, V.29 Ligand excluded by PLIP LFA.17: 5 residues within 4Å: Chain A: K.172, N.176, V.180 Ligands: LFA.7, LFA.18 Ligand excluded by PLIP LFA.18: 16 residues within 4Å: Chain A: F.153, N.176, V.179, V.180, S.183, A.184, V.187, V.188, I.191, L.207, V.210, L.211 Ligands: LFA.15, LFA.17, LFA.19, LFA.20 Ligand excluded by PLIP LFA.19: 7 residues within 4Å: Chain A: V.199, P.200, I.203, L.207 Ligands: LFA.14, LFA.18, LFA.20 Ligand excluded by PLIP LFA.20: 7 residues within 4Å: Chain A: I.203, L.206, L.207, V.210 Ligands: LFA.18, LFA.19, LFA.21 Ligand excluded by PLIP LFA.21: 1 residues within 4Å: Ligands: LFA.20 Ligand excluded by PLIP LFA.22: 10 residues within 4Å: Chain A: V.177, L.181, V.210, S.214, G.218, F.219, I.222 Ligands: LFA.6, LFA.7, SQL.11 Ligand excluded by PLIP

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

L2P.9: 15 residues within 4Å: Chain A: L.48, I.52, T.55, M.56, Y.64, T.67, W.80, Y.83, A.84, L.87, F.88, L.92, L.123, L.127 Ligands: LFA.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.52, A:W.80, A:W.80, A:W.80, A:A.84, A:L.87, A:F.88, A:F.88, A:F.88, A:L.123, A:L.123, A:L.127 Hydrogen bonds: A:Y.64

1 x SQL: (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene(Non-covalent)

SQL.11: 18 residues within 4Å: Chain A: W.12, L.15, L.19, L.22, G.23, Y.26, K.30, L.206, M.209, V.210, V.213, S.214, V.217, G.218, L.221, R.225 Ligands: LFA.4, LFA.22 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.15, A:L.19, A:L.22, A:Y.26, A:Y.26, A:V.210, A:V.213, A:V.217, A:L.221

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

2022-05-18

Peptides

Bacteriorhodopsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
P

Membrane

We predict this structure to be a membrane protein.
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Bacteriorhodopsin

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