SMTL ID : 4fpd.1 (1 other biounit)

Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 14 residues within 4Å: Chain A: W.99, T.103, L.106, M.131, G.135, W.151, S.154, T.155, M.158, W.195, Y.198, W.202, D.225, K.229 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.99, A:T.103, A:L.106, A:W.195, A:Y.198, A:Y.198, A:Y.198, A:Y.198, A:Y.198, A:W.202, A:W.202, A:K.229 RET.11: 14 residues within 4Å: Chain B: W.99, T.103, L.106, M.131, G.135, W.151, S.154, T.155, M.158, W.195, Y.198, W.202, D.225, K.229 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.99, B:T.103, B:L.106, B:W.195, B:Y.198, B:Y.198, B:Y.198, B:Y.198, B:Y.198, B:W.202, B:W.202, B:K.229 RET.21: 14 residues within 4Å: Chain C: W.99, T.103, L.106, M.131, G.135, W.151, S.154, T.155, M.158, W.195, Y.198, W.202, D.225, K.229 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.99, C:T.103, C:L.106, C:W.195, C:Y.198, C:Y.198, C:Y.198, C:Y.198, C:Y.198, C:W.202, C:W.202, C:K.229

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: T.141, W.150 Chain B: L.75, Y.77 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: T.141, W.150 Chain C: L.75, Y.77 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain A: L.75, Y.77 Chain C: T.141, W.150 Ligand excluded by PLIP

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

LI1.3: 3 residues within 4Å: Chain A: V.149 Chain B: L.71 Ligands: LI1.16 Ligand excluded by PLIP LI1.4: 7 residues within 4Å: Chain A: Y.144, S.145, F.148, V.149, W.151, A.152 Ligands: LI1.5 Ligand excluded by PLIP LI1.5: 3 residues within 4Å: Chain A: W.151, L.203 Ligands: LI1.4 Ligand excluded by PLIP LI1.6: 2 residues within 4Å: Chain A: T.30 Ligands: LI1.23 Ligand excluded by PLIP LI1.7: 12 residues within 4Å: Chain A: I.65, M.69, Y.77, W.93, L.100, F.101, L.140 Chain C: G.126, G.129, I.130, G.133, L.136 Ligand excluded by PLIP LI1.8: 2 residues within 4Å: Chain A: L.38, Y.39 Ligand excluded by PLIP LI1.9: 11 residues within 4Å: Chain A: L.41, Y.56, A.57, T.60, F.67, T.68 Chain C: A.123, I.130, I.153, A.157, Y.160 Ligand excluded by PLIP LI1.10: 4 residues within 4Å: Chain A: F.101, P.104, L.105, L.108 Ligand excluded by PLIP LI1.13: 3 residues within 4Å: Chain B: V.149 Chain C: L.71 Ligands: LI1.26 Ligand excluded by PLIP LI1.14: 7 residues within 4Å: Chain B: Y.144, S.145, F.148, V.149, W.151, A.152 Ligands: LI1.15 Ligand excluded by PLIP LI1.15: 3 residues within 4Å: Chain B: W.151, L.203 Ligands: LI1.14 Ligand excluded by PLIP LI1.16: 2 residues within 4Å: Chain B: T.30 Ligands: LI1.3 Ligand excluded by PLIP LI1.17: 12 residues within 4Å: Chain A: G.126, G.129, I.130, G.133, L.136 Chain B: I.65, M.69, Y.77, W.93, L.100, F.101, L.140 Ligand excluded by PLIP LI1.18: 2 residues within 4Å: Chain B: L.38, Y.39 Ligand excluded by PLIP LI1.19: 11 residues within 4Å: Chain A: A.123, I.130, I.153, A.157, Y.160 Chain B: L.41, Y.56, A.57, T.60, F.67, T.68 Ligand excluded by PLIP LI1.20: 4 residues within 4Å: Chain B: F.101, P.104, L.105, L.108 Ligand excluded by PLIP LI1.23: 3 residues within 4Å: Chain A: L.71 Chain C: V.149 Ligands: LI1.6 Ligand excluded by PLIP LI1.24: 7 residues within 4Å: Chain C: Y.144, S.145, F.148, V.149, W.151, A.152 Ligands: LI1.25 Ligand excluded by PLIP LI1.25: 3 residues within 4Å: Chain C: W.151, L.203 Ligands: LI1.24 Ligand excluded by PLIP LI1.26: 2 residues within 4Å: Chain C: T.30 Ligands: LI1.13 Ligand excluded by PLIP LI1.27: 12 residues within 4Å: Chain B: G.126, G.129, I.130, G.133, L.136 Chain C: I.65, M.69, Y.77, W.93, L.100, F.101, L.140 Ligand excluded by PLIP LI1.28: 2 residues within 4Å: Chain C: L.38, Y.39 Ligand excluded by PLIP LI1.29: 11 residues within 4Å: Chain B: A.123, I.130, I.153, A.157, Y.160 Chain C: L.41, Y.56, A.57, T.60, F.67, T.68 Ligand excluded by PLIP LI1.30: 4 residues within 4Å: Chain C: F.101, P.104, L.105, L.108 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, T. et al., Deprotonation of d96 in bacteriorhodopsin opens the proton uptake pathway. Structure (2013)

Release Date

2013-02-27

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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