SMTL ID : 5h2h.1

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 40 ns after photoexcitation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 19 residues within 4Å: Chain A: Y.83, W.86, T.89, T.90, L.93, M.118, I.119, G.122, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.86, 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:P.186, A:W.189, A:K.216 RET.17: 19 residues within 4Å: Chain B: Y.83, W.86, T.89, T.90, L.93, M.118, I.119, G.122, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.86, 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:P.186, B:W.189, B:K.216 RET.33: 19 residues within 4Å: Chain C: Y.83, W.86, T.89, T.90, L.93, M.118, I.119, G.122, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.86, 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:P.186, C:W.189, C:K.216

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

L2P.2: 23 residues within 4Å: Chain A: T.107, A.110, A.114, I.117, I.140, A.143, 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, T.55 Ligands: UND.16, D10.20, HP6.21 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.25, B:L.28, B:T.47, B:L.48, A:A.110, A:Y.147, A:Y.147 L2P.10: 10 residues within 4Å: Chain A: Y.131, F.135, W.138, A.139, T.142, A.143, L.146, L.190, A.196 Ligands: UND.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.135 L2P.11: 28 residues within 4Å: Chain A: L.48, I.52, T.55, M.56, Y.64, T.67, W.80, Y.83, A.84, L.87, F.88, L.92, L.123, L.127 Chain C: L.87, V.112, G.113, G.116, I.117, G.120, T.121, L.123, V.124, L.127 Ligands: C14.14, L2P.27, L2P.43, C14.46 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:I.52, A:I.52, A:W.80, A:W.80, A:W.80, A:F.88, A:L.123, C:L.87, C:I.117, C:L.123, C:V.124 Hydrogen bonds: A:Y.64 L2P.18: 23 residues within 4Å: Chain B: T.107, A.110, A.114, I.117, I.140, A.143, 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, T.55 Ligands: UND.32, D10.36, HP6.37 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:A.110, B:Y.147, B:Y.147, C:L.25, C:L.28, C:T.47, C:L.48 L2P.26: 10 residues within 4Å: Chain B: Y.131, F.135, W.138, A.139, T.142, A.143, L.146, L.190, A.196 Ligands: UND.25 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.135 L2P.27: 28 residues within 4Å: Chain A: L.87, V.112, G.113, G.116, I.117, G.120, T.121, L.123, V.124, L.127 Chain B: L.48, I.52, T.55, M.56, Y.64, T.67, W.80, Y.83, A.84, L.87, F.88, L.92, L.123, L.127 Ligands: L2P.11, C14.14, C14.30, L2P.43 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.52, B:I.52, B:W.80, B:W.80, B:W.80, B:F.88, B:L.123, A:L.87, A:I.117, A:L.123, A:V.124 Hydrogen bonds: B:Y.64 L2P.34: 23 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, T.55 Chain C: T.107, A.110, A.114, I.117, I.140, A.143, A.144, Y.147 Ligands: D10.4, HP6.5, UND.48 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:A.110, C:Y.147, C:Y.147, A:L.25, A:L.28, A:T.47, A:L.48 L2P.42: 10 residues within 4Å: Chain C: Y.131, F.135, W.138, A.139, T.142, A.143, L.146, L.190, A.196 Ligands: UND.41 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.135 L2P.43: 28 residues within 4Å: Chain B: L.87, V.112, G.113, G.116, I.117, G.120, T.121, L.123, V.124, L.127 Chain C: L.48, I.52, T.55, M.56, Y.64, T.67, W.80, Y.83, A.84, L.87, F.88, L.92, L.123, L.127 Ligands: L2P.11, L2P.27, C14.30, C14.46 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:L.87, B:I.117, B:L.123, B:V.124, C:I.52, C:I.52, C:W.80, C:W.80, C:W.80, C:F.88, C:L.123 Hydrogen bonds: C:Y.64

3 x TRD: TRIDECANE(Non-covalent)

TRD.3: 13 residues within 4Å: Chain A: W.138, T.142, M.145, L.146, L.149, Y.150, F.153, F.154, V.179, S.183, P.186, V.187 Ligands: OCT.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.146, A:L.149 TRD.19: 13 residues within 4Å: Chain B: W.138, T.142, M.145, L.146, L.149, Y.150, F.153, F.154, V.179, S.183, P.186, V.187 Ligands: OCT.23 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.146, B:L.149 TRD.35: 13 residues within 4Å: Chain C: W.138, T.142, M.145, L.146, L.149, Y.150, F.153, F.154, V.179, S.183, P.186, V.187 Ligands: OCT.39 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.146, C:L.149

3 x D10: DECANE(Non-covalent)

D10.4: 12 residues within 4Å: Chain A: W.10, A.14, T.17, A.18, G.21, L.22, L.25, F.54, L.58, L.61 Ligands: HP6.5, L2P.34 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.17, A:L.22 D10.20: 12 residues within 4Å: Chain B: W.10, A.14, T.17, A.18, G.21, L.22, L.25, F.54, L.58, L.61 Ligands: L2P.2, HP6.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.17, B:L.22 D10.36: 12 residues within 4Å: Chain C: W.10, A.14, T.17, A.18, G.21, L.22, L.25, F.54, L.58, L.61 Ligands: L2P.18, HP6.37 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.17, C:L.22

3 x HP6: HEPTANE(Non-functional Binders)

HP6.5: 10 residues within 4Å: Chain A: I.4, T.17, F.54, L.58, L.61, L.62 Chain C: V.136, I.140 Ligands: D10.4, L2P.34 No protein-ligand interaction detected (PLIP) HP6.21: 10 residues within 4Å: Chain A: V.136, I.140 Chain B: I.4, T.17, F.54, L.58, L.61, L.62 Ligands: L2P.2, D10.20 No protein-ligand interaction detected (PLIP) HP6.37: 10 residues within 4Å: Chain B: V.136, I.140 Chain C: I.4, T.17, F.54, L.58, L.61, L.62 Ligands: L2P.18, D10.36 No protein-ligand interaction detected (PLIP)

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

OCT.6: 6 residues within 4Å: Chain A: K.172, V.173, N.176, V.177, V.180 Ligands: DD9.13 No protein-ligand interaction detected (PLIP) OCT.7: 7 residues within 4Å: Chain A: V.179, V.180, S.183, A.184, V.187 Ligands: TRD.3, MYS.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.179 OCT.15: 5 residues within 4Å: Chain A: L.22, L.25, Y.26, V.29, K.30 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.26, A:Y.26, A:V.29 OCT.22: 6 residues within 4Å: Chain B: K.172, V.173, N.176, V.177, V.180 Ligands: DD9.29 No protein-ligand interaction detected (PLIP) OCT.23: 7 residues within 4Å: Chain B: V.179, V.180, S.183, A.184, V.187 Ligands: TRD.19, MYS.24 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.179 OCT.31: 5 residues within 4Å: Chain B: L.22, L.25, Y.26, V.29, K.30 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.26, B:Y.26, B:V.29 OCT.38: 6 residues within 4Å: Chain C: K.172, V.173, N.176, V.177, V.180 Ligands: DD9.45 No protein-ligand interaction detected (PLIP) OCT.39: 7 residues within 4Å: Chain C: V.179, V.180, S.183, A.184, V.187 Ligands: TRD.35, MYS.40 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.179 OCT.47: 5 residues within 4Å: Chain C: L.22, L.25, Y.26, V.29, K.30 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.26, C:Y.26, C:V.29

6 x MYS: PENTADECANE(Non-covalent)

MYS.8: 10 residues within 4Å: Chain A: A.184, V.187, V.188, I.191, I.198, V.199, P.200, I.203, L.207 Ligands: OCT.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.191 MYS.12: 11 residues within 4Å: Chain A: L.19, L.22, G.23, Y.26, V.213, S.214, V.217, G.218, L.221, R.225 Ligands: DD9.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.26, A:V.213, A:V.217 MYS.24: 10 residues within 4Å: Chain B: A.184, V.187, V.188, I.191, I.198, V.199, P.200, I.203, L.207 Ligands: OCT.23 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.191 MYS.28: 11 residues within 4Å: Chain B: L.19, L.22, G.23, Y.26, V.213, S.214, V.217, G.218, L.221, R.225 Ligands: DD9.29 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.26, B:V.213, B:V.217 MYS.40: 10 residues within 4Å: Chain C: A.184, V.187, V.188, I.191, I.198, V.199, P.200, I.203, L.207 Ligands: OCT.39 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.191 MYS.44: 11 residues within 4Å: Chain C: L.19, L.22, G.23, Y.26, V.213, S.214, V.217, G.218, L.221, R.225 Ligands: DD9.45 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.26, C:V.213, C:V.217

6 x UND: UNDECANE(Non-covalent)

UND.9: 6 residues within 4Å: Chain A: Y.131, S.132, F.135, V.136, A.139 Ligands: L2P.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.131, A:A.139 UND.16: 7 residues within 4Å: Chain A: A.143, L.146, Y.147, Y.150 Chain B: L.28, M.32 Ligands: L2P.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.150 UND.25: 6 residues within 4Å: Chain B: Y.131, S.132, F.135, V.136, A.139 Ligands: L2P.26 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.131, B:A.139 UND.32: 7 residues within 4Å: Chain B: A.143, L.146, Y.147, Y.150 Chain C: L.28, M.32 Ligands: L2P.18 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.150 UND.41: 6 residues within 4Å: Chain C: Y.131, S.132, F.135, V.136, A.139 Ligands: L2P.42 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.131, C:A.139 UND.48: 7 residues within 4Å: Chain A: L.28, M.32 Chain C: A.143, L.146, Y.147, Y.150 Ligands: L2P.34 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.150

3 x DD9: nonane(Non-covalent)

DD9.13: 9 residues within 4Å: Chain A: V.177, L.181, S.214, G.218, L.221, I.222, R.225 Ligands: OCT.6, MYS.12 No protein-ligand interaction detected (PLIP) DD9.29: 9 residues within 4Å: Chain B: V.177, L.181, S.214, G.218, L.221, I.222, R.225 Ligands: OCT.22, MYS.28 No protein-ligand interaction detected (PLIP) DD9.45: 9 residues within 4Å: Chain C: V.177, L.181, S.214, G.218, L.221, I.222, R.225 Ligands: OCT.38, MYS.44 No protein-ligand interaction detected (PLIP)

3 x C14: TETRADECANE(Non-covalent)

C14.14: 11 residues within 4Å: Chain A: L.87, F.88, P.91, L.92, L.95, I.108, L.109, V.112 Chain B: F.88 Ligands: L2P.11, L2P.27 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.87, A:P.91, A:L.95, A:I.108 C14.30: 11 residues within 4Å: Chain B: L.87, F.88, P.91, L.92, L.95, I.108, L.109, V.112 Chain C: F.88 Ligands: L2P.27, L2P.43 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.87, B:P.91, B:L.95, B:I.108 C14.46: 11 residues within 4Å: Chain A: F.88 Chain C: L.87, F.88, P.91, L.92, L.95, I.108, L.109, V.112 Ligands: L2P.11, L2P.43 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.87, C:P.91, C:L.95, C:I.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nango, E. et al., A three-dimensional movie of structural changes in bacteriorhodopsin. Science (2016)

Release Date

2016-12-21

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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