SMTL ID : 1p8u.1

BACTERIORHODOPSIN N' 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: 18 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, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 13 PLIP interactions: 13 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:W.189, A:A.215, A:K.216 RET.16: 18 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, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 13 PLIP interactions: 13 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:W.189, B:A.215, B:K.216 RET.31: 18 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, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 13 PLIP interactions: 13 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: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: 8 residues within 4Å: Chain A: Y.133, V.136, A.139, I.140 Chain B: L.58 Ligands: LI1.3, LI1.9, LI1.22 Ligand excluded by PLIP LI1.3: 8 residues within 4Å: Chain A: Y.131, F.135, V.136, A.139, L.190, A.196 Ligands: LI1.2, LI1.4 Ligand excluded by PLIP LI1.4: 6 residues within 4Å: Chain A: W.138, V.187, L.190, A.196, 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: 7 residues within 4Å: Chain A: A.14, T.17, A.18, L.22, L.61 Ligands: LI1.12, LI1.32 Ligand excluded by PLIP LI1.8: 17 residues within 4Å: Chain A: T.55, M.56, Y.64, W.80, F.88 Chain C: T.67, W.80, A.84, F.88, G.113, G.116, I.117, L.123, V.124, L.127 Ligands: LI1.23, LI1.38 Ligand excluded by PLIP LI1.9: 4 residues within 4Å: Chain A: A.139, A.143 Chain B: L.25 Ligands: LI1.2 Ligand excluded by PLIP LI1.10: 2 residues within 4Å: Chain A: L.146, F.154 Ligand excluded by PLIP LI1.11: 10 residues within 4Å: Chain A: F.153, K.172, R.175, N.176, V.179, V.180, S.183, A.184, 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: 12 residues within 4Å: Chain A: T.24, L.25, L.28, Y.43, A.44, T.47, F.54 Chain C: A.110, A.114, I.140, A.144, Y.147 Ligand excluded by PLIP LI1.14: 3 residues within 4Å: Chain A: L.87, P.91, L.95 Ligand excluded by PLIP LI1.17: 8 residues within 4Å: Chain B: Y.133, V.136, A.139, I.140 Chain C: L.58 Ligands: LI1.18, LI1.24, LI1.37 Ligand excluded by PLIP LI1.18: 8 residues within 4Å: Chain B: Y.131, F.135, V.136, A.139, L.190, A.196 Ligands: LI1.17, LI1.19 Ligand excluded by PLIP LI1.19: 6 residues within 4Å: Chain B: W.138, V.187, L.190, A.196, 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: 7 residues within 4Å: Chain B: A.14, T.17, A.18, L.22, L.61 Ligands: LI1.2, LI1.27 Ligand excluded by PLIP LI1.23: 17 residues within 4Å: Chain A: T.67, W.80, A.84, F.88, G.113, G.116, I.117, L.123, V.124, L.127 Chain B: T.55, M.56, Y.64, W.80, F.88 Ligands: LI1.8, LI1.38 Ligand excluded by PLIP LI1.24: 4 residues within 4Å: Chain B: A.139, A.143 Chain C: L.25 Ligands: LI1.17 Ligand excluded by PLIP LI1.25: 2 residues within 4Å: Chain B: L.146, F.154 Ligand excluded by PLIP LI1.26: 10 residues within 4Å: Chain B: F.153, K.172, R.175, N.176, V.179, V.180, S.183, A.184, 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: 12 residues within 4Å: Chain A: A.110, A.114, I.140, A.144, Y.147 Chain B: T.24, L.25, L.28, Y.43, A.44, T.47, F.54 Ligand excluded by PLIP LI1.29: 3 residues within 4Å: Chain B: L.87, P.91, L.95 Ligand excluded by PLIP LI1.32: 8 residues within 4Å: Chain A: L.58 Chain C: Y.133, V.136, A.139, I.140 Ligands: LI1.7, LI1.33, LI1.39 Ligand excluded by PLIP LI1.33: 8 residues within 4Å: Chain C: Y.131, F.135, V.136, A.139, L.190, A.196 Ligands: LI1.32, LI1.34 Ligand excluded by PLIP LI1.34: 6 residues within 4Å: Chain C: W.138, V.187, L.190, A.196, 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: 7 residues within 4Å: Chain C: A.14, T.17, A.18, L.22, L.61 Ligands: LI1.17, LI1.42 Ligand excluded by PLIP LI1.38: 17 residues within 4Å: Chain B: T.67, W.80, A.84, F.88, G.113, G.116, I.117, L.123, V.124, 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: L.25 Chain C: A.139, A.143 Ligands: LI1.32 Ligand excluded by PLIP LI1.40: 2 residues within 4Å: Chain C: L.146, F.154 Ligand excluded by PLIP LI1.41: 10 residues within 4Å: Chain C: F.153, K.172, R.175, N.176, V.179, V.180, S.183, A.184, 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: 12 residues within 4Å: Chain B: A.110, A.114, I.140, A.144, Y.147 Chain C: T.24, L.25, L.28, Y.43, A.44, T.47, F.54 Ligand excluded by PLIP LI1.44: 3 residues within 4Å: Chain C: L.87, P.91, L.95 Ligand excluded by PLIP

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

SQU.15: 7 residues within 4Å: Chain A: L.19, V.213, S.214, V.217, G.218, L.221, R.225 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.213, A:V.217, A:L.221, A:L.221 SQU.30: 7 residues within 4Å: Chain B: L.19, V.213, S.214, V.217, G.218, L.221, R.225 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.213, B:V.217, B:L.221, B:L.221 SQU.45: 7 residues within 4Å: Chain C: L.19, V.213, S.214, V.217, G.218, L.221, R.225 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.213, C:V.217, C:L.221, C:L.221

Links

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Citation

Schobert, B. et al., Crystallographic Structures of the M and N Intermediates of Bacteriorhodopsin: Assembly of a Hydrogen-Bonded Chain of Water Molecules between Asp-96 and the Retinal Schiff Base. J.Mol.Biol. (2003)

Release Date

2003-07-08

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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