SMTL ID : 1o0a.1

BACTERIORHODOPSIN L INTERMEDIATE AT 1.62 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: W.86, T.90, L.93, M.118, G.122, 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: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:W.189, A:A.215, A:K.216 RET.16: 16 residues within 4Å: Chain B: W.86, T.90, L.93, M.118, G.122, 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: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:W.189, B:A.215, B:K.216 RET.31: 16 residues within 4Å: Chain C: W.86, T.90, L.93, M.118, G.122, 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: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:W.189, C:A.215, C:K.216

39 x LI1: 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL(Non-covalent)(Non-functional Binders)

LI1.2: 7 residues within 4Å: Chain A: Y.133, V.136, I.140 Chain B: L.62 Ligands: LI1.3, LI1.9, LI1.22 Ligand excluded by PLIP LI1.3: 10 residues within 4Å: Chain A: Y.131, S.132, F.135, V.136, W.138, A.139, A.196 Ligands: LI1.2, LI1.4, LI1.9 Ligand excluded by PLIP LI1.4: 3 residues within 4Å: Chain A: L.190, I.198 Ligands: LI1.3 Ligand excluded by PLIP LI1.5: 2 residues within 4Å: Chain A: I.198 Ligands: LI1.11 Ligand excluded by PLIP LI1.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LI1.7: 6 residues within 4Å: Chain A: A.14, A.18, L.22, L.61 Ligands: LI1.12, LI1.32 Ligand excluded by PLIP LI1.8: 15 residues within 4Å: Chain A: T.55, M.56, Y.64, W.80, F.88 Chain B: G.120 Chain C: W.80, A.84, F.88, G.116, I.117, G.120, L.127 Ligands: LI1.23, LI1.38 Ligand excluded by PLIP LI1.9: 4 residues within 4Å: Chain A: A.139 Chain B: M.32 Ligands: LI1.2, LI1.3 Ligand excluded by PLIP LI1.10: 2 residues within 4Å: Chain A: L.146, F.154 Ligand excluded by PLIP LI1.11: 8 residues within 4Å: Chain A: F.153, K.172, N.176, V.179, V.180, S.183, V.187 Ligands: LI1.5 Ligand excluded by PLIP LI1.12: 5 residues within 4Å: Chain A: L.22, L.25, Y.26, V.29 Ligands: LI1.7 Ligand excluded by PLIP LI1.13: 14 residues within 4Å: Chain A: T.24, L.25, L.28, Y.43, A.44, T.47, L.48, A.51, F.54 Chain C: A.110, I.117, I.140, A.144, Y.147 Ligand excluded by PLIP LI1.14: 6 residues within 4Å: Chain A: L.87, F.88, L.92, L.95, I.108, V.112 Ligand excluded by PLIP LI1.17: 7 residues within 4Å: Chain B: Y.133, V.136, I.140 Chain C: L.62 Ligands: LI1.18, LI1.24, LI1.37 Ligand excluded by PLIP LI1.18: 10 residues within 4Å: Chain B: Y.131, S.132, F.135, V.136, W.138, A.139, A.196 Ligands: LI1.17, LI1.19, LI1.24 Ligand excluded by PLIP LI1.19: 3 residues within 4Å: Chain B: L.190, I.198 Ligands: LI1.18 Ligand excluded by PLIP LI1.20: 2 residues within 4Å: Chain B: I.198 Ligands: LI1.26 Ligand excluded by PLIP LI1.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LI1.22: 6 residues within 4Å: Chain B: A.14, A.18, L.22, L.61 Ligands: LI1.2, LI1.27 Ligand excluded by PLIP LI1.23: 15 residues within 4Å: Chain A: W.80, A.84, F.88, G.116, I.117, G.120, L.127 Chain B: T.55, M.56, Y.64, W.80, F.88 Chain C: G.120 Ligands: LI1.8, LI1.38 Ligand excluded by PLIP LI1.24: 4 residues within 4Å: Chain B: A.139 Chain C: M.32 Ligands: LI1.17, LI1.18 Ligand excluded by PLIP LI1.25: 2 residues within 4Å: Chain B: L.146, F.154 Ligand excluded by PLIP LI1.26: 8 residues within 4Å: Chain B: F.153, K.172, N.176, V.179, V.180, S.183, V.187 Ligands: LI1.20 Ligand excluded by PLIP LI1.27: 5 residues within 4Å: Chain B: L.22, L.25, Y.26, V.29 Ligands: LI1.22 Ligand excluded by PLIP LI1.28: 14 residues within 4Å: Chain A: A.110, I.117, I.140, A.144, Y.147 Chain B: T.24, L.25, L.28, Y.43, A.44, T.47, L.48, A.51, F.54 Ligand excluded by PLIP LI1.29: 6 residues within 4Å: Chain B: L.87, F.88, L.92, L.95, I.108, V.112 Ligand excluded by PLIP LI1.32: 7 residues within 4Å: Chain A: L.62 Chain C: Y.133, V.136, I.140 Ligands: LI1.7, LI1.33, LI1.39 Ligand excluded by PLIP LI1.33: 10 residues within 4Å: Chain C: Y.131, S.132, F.135, V.136, W.138, A.139, A.196 Ligands: LI1.32, LI1.34, LI1.39 Ligand excluded by PLIP LI1.34: 3 residues within 4Å: Chain C: L.190, I.198 Ligands: LI1.33 Ligand excluded by PLIP LI1.35: 2 residues within 4Å: Chain C: I.198 Ligands: LI1.41 Ligand excluded by PLIP LI1.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LI1.37: 6 residues within 4Å: Chain C: A.14, A.18, L.22, L.61 Ligands: LI1.17, LI1.42 Ligand excluded by PLIP LI1.38: 15 residues within 4Å: Chain A: G.120 Chain B: W.80, A.84, F.88, G.116, I.117, G.120, L.127 Chain C: T.55, M.56, Y.64, W.80, F.88 Ligands: LI1.8, LI1.23 Ligand excluded by PLIP LI1.39: 4 residues within 4Å: Chain A: M.32 Chain C: A.139 Ligands: LI1.32, LI1.33 Ligand excluded by PLIP LI1.40: 2 residues within 4Å: Chain C: L.146, F.154 Ligand excluded by PLIP LI1.41: 8 residues within 4Å: Chain C: F.153, K.172, N.176, V.179, V.180, S.183, V.187 Ligands: LI1.35 Ligand excluded by PLIP LI1.42: 5 residues within 4Å: Chain C: L.22, L.25, Y.26, V.29 Ligands: LI1.37 Ligand excluded by PLIP LI1.43: 14 residues within 4Å: Chain B: A.110, I.117, I.140, A.144, Y.147 Chain C: T.24, L.25, L.28, Y.43, A.44, T.47, L.48, A.51, F.54 Ligand excluded by PLIP LI1.44: 6 residues within 4Å: Chain C: L.87, F.88, L.92, L.95, I.108, V.112 Ligand excluded by PLIP

3 x SQU: 2,10,23-TRIMETHYL-TETRACOSANE(Non-covalent)

SQU.15: 9 residues within 4Å: Chain A: L.19, L.22, G.23, Y.26, V.210, S.214, G.218, L.221, R.225 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.19, A:L.22, A:Y.26, A:V.210, A:L.221 SQU.30: 9 residues within 4Å: Chain B: L.19, L.22, G.23, Y.26, V.210, S.214, G.218, L.221, R.225 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.19, B:L.22, B:Y.26, B:V.210, B:L.221 SQU.45: 9 residues within 4Å: Chain C: L.19, L.22, G.23, Y.26, V.210, S.214, G.218, L.221, R.225 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.19, C:L.22, C:Y.26, C:V.210, C:L.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lanyi, J.K. et al., Mechanism of proton transport in bacteriorhodopsin from crystallographic structures of theK, L, M1, M2, and M2' intermediates of the photocycle. J.Mol.Biol. (2003)

Release Date

2003-04-22

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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