SMTL ID : 7q35.1

Crystal structure of the mutant bacteriorhodopsin pressurized with krypton

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x RET: RETINAL(Covalent)

RET.1: 19 residues within 4Å: Chain A: Y.84, 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 Ligands: KR.43 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.84, A:T.91, A:L.94, A:M.146, A:W.183, A:Y.186, A:Y.186, A:Y.186, A:Y.186, A:P.187, A:P.187, A:W.190, A:A.216, A:K.217

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

LFA.2: 8 residues within 4Å: Chain A: G.22, L.23, A.52, F.55, T.56 Ligands: LFA.12, KR.38, KR.40 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.52, A:F.55, A:F.55, A:F.55, A:T.56 LFA.3: 2 residues within 4Å: Chain A: L.110 Ligands: LFA.6 No protein-ligand interaction detected (PLIP) LFA.4: 4 residues within 4Å: Chain A: G.198, I.199, V.200, P.201 No protein-ligand interaction detected (PLIP) LFA.5: 1 residues within 4Å: Ligands: OLA.14 No protein-ligand interaction detected (PLIP) LFA.6: 7 residues within 4Å: Chain A: L.88, V.113, G.117, G.121 Ligands: LFA.3, KR.24, KR.35 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.88, A:V.113 LFA.7: 4 residues within 4Å: Chain A: S.133, F.136, V.137 Ligands: KR.44 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.136 LFA.8: 6 residues within 4Å: Chain A: L.16, L.20, V.214, S.215, G.219 Ligands: KR.27 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.16, A:L.20, A:V.214 LFA.9: 4 residues within 4Å: Chain A: V.180, V.181, S.184, A.185 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.180, A:V.181, A:A.185 LFA.10: 4 residues within 4Å: Chain A: W.11, A.15, L.62 Ligands: KR.52 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.11, A:A.15, A:L.62 LFA.11: 7 residues within 4Å: Chain A: A.115, I.141, A.145, Y.148 Ligands: OLA.15, KR.23, KR.54 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.115, A:A.145, A:Y.148 LFA.12: 9 residues within 4Å: Chain A: L.29, A.45, A.48, L.49, A.52 Ligands: LFA.2, KR.32, KR.38, KR.51 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.29, A:A.45, A:A.52

3 x OLA: OLEIC ACID(Non-covalent)

OLA.13: 6 residues within 4Å: Chain A: L.147, L.150, Y.151, F.154, F.155 Ligands: HEX.18 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.151, A:F.154, A:F.154, A:F.154, A:F.154, A:F.155, A:F.155 OLA.14: 6 residues within 4Å: Chain A: G.219, L.222, I.223, R.226 Ligands: LFA.5, KR.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.222, A:I.223 Water bridges: A:I.223 Salt bridges: A:R.226 OLA.15: 3 residues within 4Å: Chain A: A.111, Y.148 Ligands: LFA.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.111 Water bridges: A:T.108

3 x HEX: HEXANE(Non-covalent)

HEX.16: 3 residues within 4Å: Chain A: F.89 Ligands: KR.46, KR.49 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.89 HEX.17: 3 residues within 4Å: Chain A: W.81, L.124, L.128 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.81, A:W.81, A:W.81 HEX.18: 4 residues within 4Å: Chain A: A.144, Y.148, Y.151 Ligands: OLA.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.151, A:Y.151, A:Y.151

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

SO4.19: 3 residues within 4Å: Chain A: T.158, K.173, R.176 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.176 Salt bridges: A:K.173, A:R.176

35 x KR: KRYPTON(Non-covalent)(Non-functional Binders)

KR.20: 6 residues within 4Å: Chain A: L.94, L.95, L.98, T.179, W.183, F.220 Ligand excluded by PLIP KR.21: 2 residues within 4Å: Chain A: A.15, L.16 Ligand excluded by PLIP KR.22: 3 residues within 4Å: Chain A: L.95, L.96, I.109 Ligand excluded by PLIP KR.23: 3 residues within 4Å: Chain A: A.115, I.118 Ligands: LFA.11 Ligand excluded by PLIP KR.24: 4 residues within 4Å: Chain A: Y.84, L.88, L.124 Ligands: LFA.6 Ligand excluded by PLIP KR.25: 4 residues within 4Å: Chain A: V.178, S.215, G.219 Ligands: OLA.14 Ligand excluded by PLIP KR.26: 3 residues within 4Å: Chain A: V.181, L.182 Ligands: KR.53 Ligand excluded by PLIP KR.27: 3 residues within 4Å: Chain A: V.218, L.222 Ligands: LFA.8 Ligand excluded by PLIP KR.28: 2 residues within 4Å: Chain A: L.110, A.111 Ligand excluded by PLIP KR.29: 1 residues within 4Å: Chain A: L.29 Ligand excluded by PLIP KR.30: 4 residues within 4Å: Chain A: S.60, Y.65, G.66, W.81 Ligand excluded by PLIP KR.31: 2 residues within 4Å: Chain A: S.60, Y.65 Ligand excluded by PLIP KR.32: 3 residues within 4Å: Chain A: A.48, L.49 Ligands: LFA.12 Ligand excluded by PLIP KR.33: 3 residues within 4Å: Chain A: T.143, P.187 Ligands: KR.34 Ligand excluded by PLIP KR.34: 2 residues within 4Å: Chain A: S.184 Ligands: KR.33 Ligand excluded by PLIP KR.35: 6 residues within 4Å: Chain A: L.88, P.92, V.113, D.116, G.117 Ligands: LFA.6 Ligand excluded by PLIP KR.36: 2 residues within 4Å: Chain A: L.110, G.114 Ligand excluded by PLIP KR.37: 3 residues within 4Å: Chain A: Y.27, K.31, L.225 Ligand excluded by PLIP KR.38: 3 residues within 4Å: Chain A: L.29 Ligands: LFA.2, LFA.12 Ligand excluded by PLIP KR.39: 3 residues within 4Å: Chain A: L.182, V.211, S.215 Ligand excluded by PLIP KR.40: 2 residues within 4Å: Chain A: T.56 Ligands: LFA.2 Ligand excluded by PLIP KR.41: 2 residues within 4Å: Chain A: T.56 Ligands: KR.48 Ligand excluded by PLIP KR.42: 3 residues within 4Å: Chain A: L.191, A.197, I.199 Ligand excluded by PLIP KR.43: 7 residues within 4Å: Chain A: T.122, G.123, G.126, W.138, W.139, W.190 Ligands: RET.1 Ligand excluded by PLIP KR.44: 3 residues within 4Å: Chain A: F.136, W.139 Ligands: LFA.7 Ligand excluded by PLIP KR.45: 2 residues within 4Å: Chain A: L.208, L.212 Ligand excluded by PLIP KR.46: 3 residues within 4Å: Chain A: P.92, L.96 Ligands: HEX.16 Ligand excluded by PLIP KR.47: 4 residues within 4Å: Chain A: M.57, A.85, F.89 Ligands: KR.48 Ligand excluded by PLIP KR.48: 4 residues within 4Å: Chain A: T.56 Ligands: KR.41, KR.47, KR.49 Ligand excluded by PLIP KR.49: 2 residues within 4Å: Ligands: HEX.16, KR.48 Ligand excluded by PLIP KR.50: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP KR.51: 3 residues within 4Å: Chain A: I.46, L.49 Ligands: LFA.12 Ligand excluded by PLIP KR.52: 3 residues within 4Å: Chain A: W.11, A.15 Ligands: LFA.10 Ligand excluded by PLIP KR.53: 4 residues within 4Å: Chain A: N.177, V.178, V.181 Ligands: KR.26 Ligand excluded by PLIP KR.54: 2 residues within 4Å: Chain A: I.141 Ligands: LFA.11 Ligand excluded by 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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