SMTL ID : 7q38.1

Crystal structure of the mutant bacteriorhodopsin pressurized with argon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x RET: RETINAL(Covalent)

RET.1: 17 residues within 4Å: Chain A: W.87, T.90, T.91, L.94, M.119, G.123, W.139, S.142, T.143, M.146, W.183, Y.186, P.187, W.190, D.213, A.216, K.217 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.91, A:L.94, A:M.146, A:W.183, A:W.183, A:Y.186, A:Y.186, A:Y.186, A:Y.186, A:P.187, A:W.190, A:A.216, A:K.217

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

LFA.2: 8 residues within 4Å: Chain A: L.147, V.181, S.184, A.185, V.188 Ligands: LFA.5, AR.35, AR.64 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.147, A:A.185, A:V.188 LFA.3: 5 residues within 4Å: Chain A: L.88, G.117, G.121, L.128 Ligands: AR.26 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.88, A:L.128 LFA.4: 9 residues within 4Å: Chain A: W.13, L.20, M.210, V.214, S.215, G.219, L.222 Ligands: OLA.14, AR.65 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.13, A:L.20, A:V.214, A:L.222 LFA.5: 6 residues within 4Å: Chain A: S.133, F.136, V.137, A.140 Ligands: LFA.2, AR.50 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.136, A:A.140 LFA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) LFA.7: 5 residues within 4Å: Chain A: I.141, A.144, A.145 Ligands: HEX.19, AR.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.141, A:A.145 LFA.8: 4 residues within 4Å: Chain A: W.81, L.124, L.128 Ligands: AR.66 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.81, A:W.81, A:L.124, A:L.128 LFA.9: 11 residues within 4Å: Chain A: L.26, L.29, A.45, A.48, L.49, A.52 Ligands: OLC.12, AR.33, AR.39, AR.45, AR.57 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.26, A:L.29, A:L.29, A:A.45, A:L.49, A:L.49, A:A.52 LFA.10: 4 residues within 4Å: Chain A: T.6, L.59, L.63 Ligands: OLA.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.59, A:L.63 LFA.11: 1 residues within 4Å: Ligands: OLA.15 No protein-ligand interaction detected (PLIP)

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

OLC.12: 14 residues within 4Å: Chain A: A.19, G.22, A.25, L.26, A.52, F.55, T.56 Ligands: LFA.9, OLA.15, AR.23, AR.39, AR.55, AR.61, AR.62 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.55 Hydrogen bonds: A:A.52

3 x OLA: OLEIC ACID(Non-covalent)

OLA.13: 4 residues within 4Å: Chain A: L.150, Y.151, F.154, F.155 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.154, A:F.154, A:F.154, A:F.155 OLA.14: 8 residues within 4Å: Chain A: L.20, G.24, Y.27, V.214, V.218, R.226 Ligands: LFA.4, AR.65 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.20, A:Y.27, A:Y.27, A:V.214, A:V.218 Salt bridges: A:R.226 OLA.15: 9 residues within 4Å: Chain A: T.6, W.11, A.15, A.19, L.62 Ligands: LFA.10, LFA.11, OLC.12, AR.61 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.6, A:W.11, A:A.15, A:L.62

4 x HEX: HEXANE(Non-covalent)

HEX.16: 2 residues within 4Å: Chain A: I.223 Ligands: HEX.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.223 HEX.17: 6 residues within 4Å: Chain A: G.219, L.222, I.223, R.226 Ligands: HEX.16, AR.27 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.222, A:I.223 HEX.18: 3 residues within 4Å: Chain A: Y.65, G.66, W.81 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.65 HEX.19: 4 residues within 4Å: Chain A: A.144, Y.148, Y.151 Ligands: LFA.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.151

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.20: 3 residues within 4Å: Chain A: T.158, K.173, R.176 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.173, A:R.176 Salt bridges: A:K.173, A:R.176 SO4.21: 5 residues within 4Å: Chain A: F.72, G.73, K.130, V.131, Y.132 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.73, A:Y.132

47 x AR: ARGON(Non-covalent)(Non-functional Binders)

AR.22: 6 residues within 4Å: Chain A: L.94, L.95, L.98, T.179, W.183, F.220 No protein-ligand interaction detected (PLIP) AR.23: 5 residues within 4Å: Chain A: A.15, L.16, A.19 Ligands: OLC.12, AR.60 No protein-ligand interaction detected (PLIP) AR.24: 3 residues within 4Å: Chain A: L.95, L.96, I.109 No protein-ligand interaction detected (PLIP) AR.25: 3 residues within 4Å: Chain A: A.115, I.118 Ligands: LFA.7 No protein-ligand interaction detected (PLIP) AR.26: 6 residues within 4Å: Chain A: Y.84, L.88, I.120, L.124 Ligands: LFA.3, AR.66 No protein-ligand interaction detected (PLIP) AR.27: 6 residues within 4Å: Chain A: V.178, S.215, G.219, F.220, I.223 Ligands: HEX.17 No protein-ligand interaction detected (PLIP) AR.28: 2 residues within 4Å: Chain A: L.182 Ligands: AR.47 No protein-ligand interaction detected (PLIP) AR.29: 2 residues within 4Å: Chain A: L.110, A.111 No protein-ligand interaction detected (PLIP) AR.30: 1 residues within 4Å: Chain A: L.29 No protein-ligand interaction detected (PLIP) AR.31: 5 residues within 4Å: Chain A: S.60, Y.65, G.66, W.81 Ligands: AR.44 No protein-ligand interaction detected (PLIP) AR.32: 3 residues within 4Å: Chain A: S.60, Y.65 Ligands: AR.44 No protein-ligand interaction detected (PLIP) AR.33: 6 residues within 4Å: Chain A: A.48, L.49, A.52 Ligands: LFA.9, AR.39, AR.45 No protein-ligand interaction detected (PLIP) AR.34: 3 residues within 4Å: Chain A: W.139, P.187 Ligands: AR.64 No protein-ligand interaction detected (PLIP) AR.35: 4 residues within 4Å: Chain A: S.184, V.188 Ligands: LFA.2, AR.64 No protein-ligand interaction detected (PLIP) AR.36: 5 residues within 4Å: Chain A: L.88, P.92, V.113, D.116, G.117 No protein-ligand interaction detected (PLIP) AR.37: 2 residues within 4Å: Chain A: L.110, G.114 No protein-ligand interaction detected (PLIP) AR.38: 4 residues within 4Å: Chain A: Y.27, F.28, K.31, L.225 No protein-ligand interaction detected (PLIP) AR.39: 4 residues within 4Å: Chain A: A.52 Ligands: LFA.9, OLC.12, AR.33 No protein-ligand interaction detected (PLIP) AR.40: 3 residues within 4Å: Chain A: L.208, V.211, L.212 No protein-ligand interaction detected (PLIP) AR.41: 6 residues within 4Å: Chain A: L.182, V.211, L.212, S.215 Ligands: AR.46, AR.47 No protein-ligand interaction detected (PLIP) AR.42: 6 residues within 4Å: Chain A: R.83, Y.84, W.87, W.190, E.195, F.209 No protein-ligand interaction detected (PLIP) AR.43: 5 residues within 4Å: Chain A: I.53, M.57, A.85, F.89 Ligands: AR.54 No protein-ligand interaction detected (PLIP) AR.44: 4 residues within 4Å: Chain A: M.57, S.60 Ligands: AR.31, AR.32 No protein-ligand interaction detected (PLIP) AR.45: 3 residues within 4Å: Chain A: L.29 Ligands: LFA.9, AR.33 No protein-ligand interaction detected (PLIP) AR.46: 6 residues within 4Å: Chain A: V.181, L.182, A.185, L.212 Ligands: AR.41, AR.47 No protein-ligand interaction detected (PLIP) AR.47: 3 residues within 4Å: Ligands: AR.28, AR.41, AR.46 No protein-ligand interaction detected (PLIP) AR.48: 5 residues within 4Å: Chain A: R.83, L.202, E.205, T.206, F.209 No protein-ligand interaction detected (PLIP) AR.49: 6 residues within 4Å: Chain A: T.122, G.123, G.126, W.138, W.139, W.190 No protein-ligand interaction detected (PLIP) AR.50: 3 residues within 4Å: Chain A: F.136, W.139 Ligands: LFA.5 No protein-ligand interaction detected (PLIP) AR.51: 3 residues within 4Å: Chain A: L.191, A.197, I.199 No protein-ligand interaction detected (PLIP) AR.52: 3 residues within 4Å: Chain A: L.153, R.176, V.180 No protein-ligand interaction detected (PLIP) AR.53: 5 residues within 4Å: Chain A: T.108, A.111, Y.148, V.152 Ligands: AR.59 No protein-ligand interaction detected (PLIP) AR.54: 3 residues within 4Å: Chain A: I.53, T.56 Ligands: AR.43 No protein-ligand interaction detected (PLIP) AR.55: 4 residues within 4Å: Chain A: A.52, I.53, T.56 Ligands: OLC.12 No protein-ligand interaction detected (PLIP) AR.56: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) AR.57: 4 residues within 4Å: Chain A: A.45, I.46, L.49 Ligands: LFA.9 No protein-ligand interaction detected (PLIP) AR.58: 3 residues within 4Å: Chain A: A.104, F.157, K.160 No protein-ligand interaction detected (PLIP) AR.59: 5 residues within 4Å: Chain A: A.111, L.112, Y.148, V.152 Ligands: AR.53 No protein-ligand interaction detected (PLIP) AR.60: 4 residues within 4Å: Chain A: I.12, A.15, L.16 Ligands: AR.23 No protein-ligand interaction detected (PLIP) AR.61: 4 residues within 4Å: Chain A: W.11, A.15 Ligands: OLC.12, OLA.15 No protein-ligand interaction detected (PLIP) AR.62: 2 residues within 4Å: Chain A: T.56 Ligands: OLC.12 No protein-ligand interaction detected (PLIP) AR.63: 3 residues within 4Å: Chain A: N.177, V.178, V.181 No protein-ligand interaction detected (PLIP) AR.64: 5 residues within 4Å: Chain A: M.146, S.184 Ligands: LFA.2, AR.34, AR.35 No protein-ligand interaction detected (PLIP) AR.65: 5 residues within 4Å: Chain A: V.214, V.218, G.219 Ligands: LFA.4, OLA.14 No protein-ligand interaction detected (PLIP) AR.66: 5 residues within 4Å: Chain A: W.81, A.85, L.124 Ligands: LFA.8, AR.26 No protein-ligand interaction detected (PLIP) AR.67: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) AR.68: 2 residues within 4Å: Chain A: L.208, V.211 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Melnikov, I. et al., High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action. Commun Biol (2022)

Release Date

2022-04-27

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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