SMTL ID : 6ga3.1

Bacteriorhodopsin, 33 ms state, ensemble refinement

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 17 residues within 4Å: Chain A: Y.83, 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.83, A:T.90, A:L.93, A:M.145, 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:A.215, A:K.216 RET.16: 17 residues within 4Å: Chain B: Y.83, 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 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.83, B:T.90, B:L.93, B:M.145, 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:A.215, B:K.216 RET.31: 17 residues within 4Å: Chain C: Y.83, 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 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:Y.83, C:T.90, C:L.93, C:M.145, 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:A.215, C:K.216

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

L2P.2: 18 residues within 4Å: Chain A: T.107, A.110, A.144, Y.147 Chain B: G.21, T.24, L.25, L.28, K.40, Y.43, A.44, T.47, L.48, A.51, F.54 Ligands: UND.15, D10.19, HP6.20 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.24, B:L.25, B:L.28, B:T.47, B:L.48, B:A.51, B:F.54, B:F.54, B:F.54, A:A.110, A:Y.147, A:Y.147 Water bridges: B:T.47 L2P.10: 9 residues within 4Å: Chain A: Y.131, F.135, W.138, A.139, A.143, L.146, L.190, A.196 Ligands: UND.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.135, A:F.135, A:W.138, A:A.139, A:A.143, A:L.146, A:L.190 L2P.11: 17 residues within 4Å: Chain A: I.52, M.56, Y.64, W.80, A.84, L.87, F.88, L.123 Chain C: L.87, G.116, I.117, G.120, L.123, V.124 Ligands: L2P.26, L2P.41, C14.43 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:I.52, A:I.52, A:W.80, A:W.80, A:W.80, A:L.87, A:F.88, A:F.88, A:L.123, C:L.87, C:I.117, C:L.123, C:V.124 Hydrogen bonds: A:Y.64 Water bridges: C:L.127 L2P.17: 18 residues within 4Å: Chain B: T.107, A.110, A.144, Y.147 Chain C: G.21, T.24, L.25, L.28, K.40, Y.43, A.44, T.47, L.48, A.51, F.54 Ligands: UND.30, D10.34, HP6.35 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:A.110, B:Y.147, B:Y.147, C:T.24, C:L.25, C:L.28, C:T.47, C:L.48, C:A.51, C:F.54, C:F.54, C:F.54 Water bridges: C:T.47 L2P.25: 9 residues within 4Å: Chain B: Y.131, F.135, W.138, A.139, A.143, L.146, L.190, A.196 Ligands: UND.24 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.135, B:F.135, B:W.138, B:A.139, B:A.143, B:L.146, B:L.190 L2P.26: 17 residues within 4Å: Chain A: L.87, G.116, I.117, G.120, L.123, V.124 Chain B: I.52, M.56, Y.64, W.80, A.84, L.87, F.88, L.123 Ligands: L2P.11, C14.13, L2P.41 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:L.87, A:I.117, A:L.123, A:V.124, B:I.52, B:I.52, B:W.80, B:W.80, B:W.80, B:L.87, B:F.88, B:F.88, B:L.123 Water bridges: A:L.127 Hydrogen bonds: B:Y.64 L2P.32: 18 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 Chain C: T.107, A.110, A.144, Y.147 Ligands: D10.4, HP6.5, UND.45 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:T.24, A:L.25, A:L.28, A:T.47, A:L.48, A:A.51, A:F.54, A:F.54, A:F.54, C:A.110, C:Y.147, C:Y.147 Water bridges: A:T.47 L2P.40: 9 residues within 4Å: Chain C: Y.131, F.135, W.138, A.139, A.143, L.146, L.190, A.196 Ligands: UND.39 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.135, C:F.135, C:W.138, C:A.139, C:A.143, C:L.146, C:L.190 L2P.41: 17 residues within 4Å: Chain B: L.87, G.116, I.117, G.120, L.123, V.124 Chain C: I.52, M.56, Y.64, W.80, A.84, L.87, F.88, L.123 Ligands: L2P.11, L2P.26, C14.28 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:I.52, C:I.52, C:W.80, C:W.80, C:W.80, C:L.87, C:F.88, C:F.88, C:L.123, B:L.87, B:I.117, B:L.123, B:V.124 Hydrogen bonds: C:Y.64 Water bridges: B:L.127

3 x TRD: TRIDECANE(Non-covalent)

TRD.3: 4 residues within 4Å: Chain A: M.145, L.146, L.149, S.183 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.149 TRD.18: 4 residues within 4Å: Chain B: M.145, L.146, L.149, S.183 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.149 TRD.33: 4 residues within 4Å: Chain C: M.145, L.146, L.149, S.183 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.149

3 x D10: DECANE(Non-covalent)

D10.4: 5 residues within 4Å: Chain A: T.17, A.18, L.22 Ligands: HP6.5, L2P.32 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.17, A:L.22 D10.19: 5 residues within 4Å: Chain B: T.17, A.18, L.22 Ligands: L2P.2, HP6.20 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.17, B:L.22 D10.34: 5 residues within 4Å: Chain C: T.17, A.18, L.22 Ligands: L2P.17, HP6.35 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.17, C:L.22

3 x HP6: HEPTANE(Non-covalent)

HP6.5: 3 residues within 4Å: Chain A: F.54 Ligands: D10.4, L2P.32 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.54 HP6.20: 3 residues within 4Å: Chain B: F.54 Ligands: L2P.2, D10.19 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.54 HP6.35: 3 residues within 4Å: Chain C: F.54 Ligands: L2P.17, D10.34 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.54

9 x OCT: N-OCTANE(Non-covalent)

OCT.6: 3 residues within 4Å: Chain A: K.172, N.176, V.177 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.176, A:V.177 OCT.7: 5 residues within 4Å: Chain A: V.179, V.180, S.183, A.184 Ligands: MYS.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.179, A:V.180 OCT.14: 2 residues within 4Å: Chain A: Y.26, V.29 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.26, A:V.29 OCT.21: 3 residues within 4Å: Chain B: K.172, N.176, V.177 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.176, B:V.177 OCT.22: 5 residues within 4Å: Chain B: V.179, V.180, S.183, A.184 Ligands: MYS.23 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.179, B:V.180 OCT.29: 2 residues within 4Å: Chain B: Y.26, V.29 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.26, B:V.29 OCT.36: 3 residues within 4Å: Chain C: K.172, N.176, V.177 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.176, C:V.177 OCT.37: 5 residues within 4Å: Chain C: V.179, V.180, S.183, A.184 Ligands: MYS.38 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.179, C:V.180 OCT.44: 2 residues within 4Å: Chain C: Y.26, V.29 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.26, C:V.29

3 x MYS: PENTADECANE(Non-covalent)

MYS.8: 4 residues within 4Å: Chain A: I.191, P.200, L.207 Ligands: OCT.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.191, A:P.200, A:L.207 MYS.23: 4 residues within 4Å: Chain B: I.191, P.200, L.207 Ligands: OCT.22 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.191, B:P.200, B:L.207 MYS.38: 4 residues within 4Å: Chain C: I.191, P.200, L.207 Ligands: OCT.37 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.191, C:P.200, C:L.207

6 x UND: UNDECANE(Non-covalent)

UND.9: 4 residues within 4Å: Chain A: Y.131, S.132, A.139 Ligands: L2P.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.131, A:A.139 UND.15: 3 residues within 4Å: Chain A: A.143, Y.150 Ligands: L2P.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.150 UND.24: 4 residues within 4Å: Chain B: Y.131, S.132, A.139 Ligands: L2P.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.131, B:A.139 UND.30: 3 residues within 4Å: Chain B: A.143, Y.150 Ligands: L2P.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.150 UND.39: 4 residues within 4Å: Chain C: Y.131, S.132, A.139 Ligands: L2P.40 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.131, C:A.139 UND.45: 3 residues within 4Å: Chain C: A.143, Y.150 Ligands: L2P.32 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.150

3 x DD9: nonane(Non-covalent)

DD9.12: 5 residues within 4Å: Chain A: V.177, L.181, G.218, L.221, R.225 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.177, A:L.181, A:L.221 DD9.27: 5 residues within 4Å: Chain B: V.177, L.181, G.218, L.221, R.225 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.177, B:L.181, B:L.221 DD9.42: 5 residues within 4Å: Chain C: V.177, L.181, G.218, L.221, R.225 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.177, C:L.181, C:L.221

3 x C14: TETRADECANE(Non-covalent)

C14.13: 5 residues within 4Å: Chain A: L.87, P.91, L.95, I.108 Ligands: L2P.26 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.87, A:P.91, A:L.95, A:L.95 C14.28: 5 residues within 4Å: Chain B: L.87, P.91, L.95, I.108 Ligands: L2P.41 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.87, B:P.91, B:L.95, B:L.95 C14.43: 5 residues within 4Å: Chain C: L.87, P.91, L.95, I.108 Ligands: L2P.11 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.87, C:P.91, C:L.95, C:L.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nass Kovacs, G. et al., Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin. Nat Commun (2019)

Release Date

2019-04-24

Peptides

Bacteriorhodopsin: 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

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