SMTL ID : 1x0i.1

Crystal Structure of the Acid Blue Form of Bacteriorhodopsin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: P.77, I.78, R.82, S.193, E.194, L.201, E.204 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:I.78, A:S.193 Water bridges: A:R.82, A:R.82, A:R.82, A:R.82, A:R.82, A:W.189 Salt bridges: A:R.82 SO4.7: 7 residues within 4Å: Chain B: P.77, I.78, R.82, S.193, E.194, L.201, E.204 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:I.78, B:S.193 Water bridges: B:R.82, B:R.82, B:R.82, B:R.82, B:R.82, B:W.189 Salt bridges: B:R.82 SO4.13: 7 residues within 4Å: Chain C: P.77, I.78, R.82, S.193, E.194, L.201, E.204 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:I.78, C:S.193 Water bridges: C:R.82, C:R.82, C:R.82, C:R.82, C:R.82, C:W.189 Salt bridges: C:R.82

3 x RET: RETINAL(Covalent)

RET.2: 16 residues within 4Å: Chain A: W.86, T.89, T.90, L.93, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: 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:P.186, A:W.189, A:W.189, A:W.189, A:A.215, A:K.216 RET.8: 16 residues within 4Å: Chain B: W.86, T.89, T.90, L.93, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: 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:P.186, B:W.189, B:W.189, B:W.189, B:A.215, B:K.216 RET.14: 16 residues within 4Å: Chain C: W.86, T.89, T.90, L.93, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: 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:P.186, C:W.189, C:W.189, C:W.189, C:A.215, C:K.216

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

L3P.3: 15 residues within 4Å: Chain A: G.21, L.25, L.28, M.32, K.40, A.44, T.47, F.54 Chain C: T.107, A.110, I.117, I.140, A.144, Y.147 Ligands: L3P.17 11 PLIP interactions: 5 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:A.110, C:I.117, C:I.140, C:Y.147, A:L.25, A:L.28, A:T.47, A:F.54 Hydrogen bonds: C:T.107 Water bridges: A:T.47 Salt bridges: A:K.40 L3P.5: 6 residues within 4Å: Chain A: V.136, A.139, I.140 Chain B: L.61, L.62 Ligands: L3P.9 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:A.139, B:L.61, B:L.62 L3P.6: 3 residues within 4Å: Chain A: F.135, L.146, S.183 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.135, A:L.146 L3P.9: 15 residues within 4Å: Chain A: T.107, A.110, I.117, I.140, A.144, Y.147 Chain B: G.21, L.25, L.28, M.32, K.40, A.44, T.47, F.54 Ligands: L3P.5 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.110, A:I.117, A:I.140, A:Y.147, B:L.25, B:L.28, B:T.47, B:F.54 Hydrogen bonds: A:T.107 Water bridges: B:T.47 Salt bridges: B:K.40 L3P.11: 6 residues within 4Å: Chain B: V.136, A.139, I.140 Chain C: L.61, L.62 Ligands: L3P.15 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.61, C:L.62, B:A.139 L3P.12: 3 residues within 4Å: Chain B: F.135, L.146, S.183 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.135, B:L.146 L3P.15: 15 residues within 4Å: Chain B: T.107, A.110, I.117, I.140, A.144, Y.147 Chain C: G.21, L.25, L.28, M.32, K.40, A.44, T.47, F.54 Ligands: L3P.11 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.25, C:L.28, C:T.47, C:F.54, B:A.110, B:I.117, B:I.140, B:Y.147 Water bridges: C:T.47 Salt bridges: C:K.40 Hydrogen bonds: B:T.107 L3P.17: 6 residues within 4Å: Chain A: L.61, L.62 Chain C: V.136, A.139, I.140 Ligands: L3P.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.61, A:L.62, C:A.139 L3P.18: 3 residues within 4Å: Chain C: F.135, L.146, S.183 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.135, C:L.146

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

L2P.4: 13 residues within 4Å: Chain A: W.80, G.116, I.117, G.120, T.121, L.123, V.124, L.127 Chain B: I.52, T.55, M.56, F.88, L.92 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.52, B:F.88, B:L.92, A:L.123, A:V.124 L2P.10: 13 residues within 4Å: Chain B: W.80, G.116, I.117, G.120, T.121, L.123, V.124, L.127 Chain C: I.52, T.55, M.56, F.88, L.92 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.52, C:F.88, C:L.92, B:L.123, B:V.124 L2P.16: 13 residues within 4Å: Chain A: I.52, T.55, M.56, F.88, L.92 Chain C: W.80, G.116, I.117, G.120, T.121, L.123, V.124, L.127 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:L.123, C:V.124, A:I.52, A:F.88, A:L.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okumura, H. et al., Crystal Structures of Acid Blue and Alkaline Purple Forms of Bacteriorhodopsin. J.Mol.Biol. (2005)

Release Date

2005-08-02

Peptides

Bacteriorhodopsin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
1

C
1

Membrane

We predict this structure to be a membrane protein.
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Bacteriorhodopsin

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