SMTL ID : 3nsb.1

Structure of bacteriorhodopsin ground state before and after X-ray modification

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 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 14 PLIP interactions: 14 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:P.186, A:W.189, A:W.189, A:A.215, A:K.216 RET.11: 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 14 PLIP interactions: 14 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:P.186, B:W.189, B:W.189, B:A.215, B:K.216 RET.21: 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 14 PLIP interactions: 14 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:P.186, C:W.189, C:W.189, C:A.215, C:K.216

27 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: 10 residues within 4Å: Chain A: L.28, A.44, T.47, F.54 Chain B: A.110, A.114, I.117, I.140, A.144, Y.147 Ligand excluded by PLIP LI1.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LI1.4: 3 residues within 4Å: Chain A: W.80, A.84, L.123 Ligand excluded by PLIP LI1.5: 5 residues within 4Å: Chain A: L.48, I.52, F.88 Chain B: G.113, G.116 Ligand excluded by PLIP LI1.6: 2 residues within 4Å: Chain A: Y.64, W.80 Ligand excluded by PLIP LI1.7: 1 residues within 4Å: Ligands: LI1.10 Ligand excluded by PLIP LI1.8: 2 residues within 4Å: Chain A: I.203 Ligands: LI1.9 Ligand excluded by PLIP LI1.9: 2 residues within 4Å: Chain A: I.198 Ligands: LI1.8 Ligand excluded by PLIP LI1.10: 3 residues within 4Å: Chain A: A.18, L.61 Ligands: LI1.7 Ligand excluded by PLIP LI1.12: 10 residues within 4Å: Chain B: L.28, A.44, T.47, F.54 Chain C: A.110, A.114, I.117, I.140, A.144, Y.147 Ligand excluded by PLIP LI1.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LI1.14: 3 residues within 4Å: Chain B: W.80, A.84, L.123 Ligand excluded by PLIP LI1.15: 5 residues within 4Å: Chain B: L.48, I.52, F.88 Chain C: G.113, G.116 Ligand excluded by PLIP LI1.16: 2 residues within 4Å: Chain B: Y.64, W.80 Ligand excluded by PLIP LI1.17: 1 residues within 4Å: Ligands: LI1.20 Ligand excluded by PLIP LI1.18: 2 residues within 4Å: Chain B: I.203 Ligands: LI1.19 Ligand excluded by PLIP LI1.19: 2 residues within 4Å: Chain B: I.198 Ligands: LI1.18 Ligand excluded by PLIP LI1.20: 3 residues within 4Å: Chain B: A.18, L.61 Ligands: LI1.17 Ligand excluded by PLIP LI1.22: 10 residues within 4Å: Chain A: A.110, A.114, I.117, I.140, A.144, Y.147 Chain C: L.28, A.44, T.47, F.54 Ligand excluded by PLIP LI1.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LI1.24: 3 residues within 4Å: Chain C: W.80, A.84, L.123 Ligand excluded by PLIP LI1.25: 5 residues within 4Å: Chain A: G.113, G.116 Chain C: L.48, I.52, F.88 Ligand excluded by PLIP LI1.26: 2 residues within 4Å: Chain C: Y.64, W.80 Ligand excluded by PLIP LI1.27: 1 residues within 4Å: Ligands: LI1.30 Ligand excluded by PLIP LI1.28: 2 residues within 4Å: Chain C: I.203 Ligands: LI1.29 Ligand excluded by PLIP LI1.29: 2 residues within 4Å: Chain C: I.198 Ligands: LI1.28 Ligand excluded by PLIP LI1.30: 3 residues within 4Å: Chain C: A.18, L.61 Ligands: LI1.27 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borshchevskiy, V.I. et al., X-ray-Radiation-Induced Changes in Bacteriorhodopsin Structure. J.Mol.Biol. (2011)

Release Date

2011-05-11

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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