SMTL ID : 1dze.1

Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x GLC- MAN- GAL: beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose

GLC-MAN-GAL.1: 9 residues within 4Å: Chain A: T.67, V.69, L.127, K.129 Chain C: Y.64, L.66, T.67, W.80 Ligands: L2P.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.67, A:K.129, A:K.129, A:K.129, C:L.66, C:T.67 GLC-MAN-GAL.8: 9 residues within 4Å: Chain A: Y.64, L.66, T.67, W.80 Chain B: T.67, V.69, L.127, K.129 Ligands: L2P.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.67, B:K.129, B:K.129, B:K.129, A:L.66, A:T.67 GLC-MAN-GAL.15: 9 residues within 4Å: Chain B: Y.64, L.66, T.67, W.80 Chain C: T.67, V.69, L.127, K.129 Ligands: L2P.18 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.67, C:K.129, B:L.66, B:T.67, C:K.129, C:K.129

3 x RET: RETINAL(Covalent)

RET.2: 16 residues within 4Å: Chain A: Y.83, W.86, T.89, T.90, L.93, M.118, G.122, W.138, S.141, T.142, W.182, Y.185, P.186, W.189, A.215, K.216 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.83, A:W.86, A:T.89, A:T.90, A:L.93, A:W.182, A:W.182, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:P.186, A:W.189, A:K.216 RET.9: 16 residues within 4Å: Chain B: Y.83, W.86, T.89, T.90, L.93, M.118, G.122, W.138, S.141, T.142, W.182, Y.185, P.186, W.189, A.215, K.216 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.83, B:W.86, B:T.89, B:T.90, B:L.93, B:W.182, B:W.182, B:Y.185, B:Y.185, B:Y.185, B:Y.185, B:Y.185, B:P.186, B:W.189, B:K.216 RET.16: 16 residues within 4Å: Chain C: Y.83, W.86, T.89, T.90, L.93, M.118, G.122, W.138, S.141, T.142, W.182, Y.185, P.186, W.189, A.215, K.216 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Y.83, C:W.86, C:T.89, C:T.90, C:L.93, C:W.182, C:W.182, C:Y.185, C:Y.185, C:Y.185, C:Y.185, C:Y.185, C:P.186, C:W.189, C:K.216

3 x L1P: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL(Non-covalent)

L1P.3: 15 residues within 4Å: Chain A: T.24, L.28, K.40, Y.43, A.44, T.47, L.48, A.51 Chain B: T.107, A.110, A.114, I.117, A.144, Y.147, Y.150 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:A.110, B:A.114, B:I.117, B:A.144, B:Y.147, B:Y.150, A:T.24, A:L.28, A:A.44, A:A.51 Salt bridges: A:K.40 L1P.10: 15 residues within 4Å: Chain B: T.24, L.28, K.40, Y.43, A.44, T.47, L.48, A.51 Chain C: T.107, A.110, A.114, I.117, A.144, Y.147, Y.150 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:T.24, B:L.28, B:A.44, B:A.51, C:A.110, C:A.114, C:I.117, C:A.144, C:Y.147, C:Y.150 Salt bridges: B:K.40 L1P.17: 15 residues within 4Å: Chain A: T.107, A.110, A.114, I.117, A.144, Y.147, Y.150 Chain C: T.24, L.28, K.40, Y.43, A.44, T.47, L.48, A.51 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:T.24, C:L.28, C:A.44, C:A.51, A:A.110, A:A.114, A:I.117, A:A.144, A:Y.147, A:Y.150 Salt bridges: C:K.40

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

L2P.4: 17 residues within 4Å: Chain A: L.109, G.113, I.117, G.120, V.124, L.127 Chain C: I.52, T.55, M.56, Y.64, W.80, A.84, L.87, F.88, L.123 Ligands: GLC-MAN-GAL.1, GLC-MAN-GAL.1 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:I.52, C:W.80, C:W.80, C:A.84, C:L.87, C:F.88, C:F.88, C:L.123, A:L.109, A:I.117, A:V.124 L2P.7: 5 residues within 4Å: Chain A: Y.26, V.29, K.30, V.217, L.221 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.26, A:Y.26, A:V.217, A:L.221 L2P.11: 17 residues within 4Å: Chain A: I.52, T.55, M.56, Y.64, W.80, A.84, L.87, F.88, L.123 Chain B: L.109, G.113, I.117, G.120, V.124, L.127 Ligands: GLC-MAN-GAL.8, GLC-MAN-GAL.8 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:L.109, B:I.117, B:V.124, A:I.52, A:W.80, A:W.80, A:A.84, A:L.87, A:F.88, A:F.88, A:L.123 L2P.14: 5 residues within 4Å: Chain B: Y.26, V.29, K.30, V.217, L.221 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.26, B:Y.26, B:V.217, B:L.221 L2P.18: 17 residues within 4Å: Chain B: I.52, T.55, M.56, Y.64, W.80, A.84, L.87, F.88, L.123 Chain C: L.109, G.113, I.117, G.120, V.124, L.127 Ligands: GLC-MAN-GAL.15, GLC-MAN-GAL.15 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.52, B:W.80, B:W.80, B:A.84, B:L.87, B:F.88, B:F.88, B:L.123, C:L.109, C:I.117, C:V.124 L2P.21: 5 residues within 4Å: Chain C: Y.26, V.29, K.30, V.217, L.221 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.26, C:Y.26, C:V.217, C:L.221

3 x L3P: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE(Non-covalent)

L3P.5: 16 residues within 4Å: Chain A: G.6, R.7, W.10, A.14, T.17, A.18, F.54, L.58, M.60, L.61, L.62, G.63 Chain B: Y.133, A.139, I.140, A.143 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.139, B:I.140, B:A.143, A:T.17, A:A.18, A:F.54 Hydrogen bonds: B:Y.133, A:G.6 Water bridges: A:R.7, A:R.7 L3P.12: 16 residues within 4Å: Chain B: G.6, R.7, W.10, A.14, T.17, A.18, F.54, L.58, M.60, L.61, L.62, G.63 Chain C: Y.133, A.139, I.140, A.143 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:A.139, C:I.140, C:A.143, B:T.17, B:A.18, B:F.54 Hydrogen bonds: C:Y.133, B:G.6 Water bridges: B:R.7, B:R.7 L3P.19: 16 residues within 4Å: Chain A: Y.133, A.139, I.140, A.143 Chain C: G.6, R.7, W.10, A.14, T.17, A.18, F.54, L.58, M.60, L.61, L.62, G.63 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:T.17, C:A.18, C:F.54, A:A.139, A:I.140, A:A.143 Hydrogen bonds: C:G.6, A:Y.133 Water bridges: C:R.7, C:R.7

3 x L4P: 3-[GLYCEROLYLPHOSPHONYL]-[1,2-DI-PHYTANYL]GLYCEROL(Non-covalent)

L4P.6: 7 residues within 4Å: Chain A: Y.131, F.135, W.138, A.139, L.190, A.196, G.197 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.139, A:L.190 Hydrogen bonds: A:Y.131 L4P.13: 7 residues within 4Å: Chain B: Y.131, F.135, W.138, A.139, L.190, A.196, G.197 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.139, B:L.190 Hydrogen bonds: B:Y.131 L4P.20: 7 residues within 4Å: Chain C: Y.131, F.135, W.138, A.139, L.190, A.196, G.197 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.139, C:L.190 Hydrogen bonds: C:Y.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takeda, K. et al., Crystal Structure of the M Intermediate of Bacteriorhodopsin: Allosteric Structural Changes Mediated by Sliding Movement of a Transmembrane Helix. J.Mol.Biol. (2004)

Release Date

2000-08-16

Peptides

BACTERIORHODOPSIN (M INTERMEDIATE): ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
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BACTERIORHODOPSIN (M INTERMEDIATE)

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