SMTL ID : 4y9h.1

The 1.43 angstrom crystal structure of bacteriorhodopsin crystallized from bicelles

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

1 x RET: RETINAL(Covalent)

RET.1: 17 residues within 4Å: Chain A: Y.78, W.81, T.85, L.88, M.113, G.117, W.133, S.136, T.137, M.140, W.177, Y.180, P.181, W.184, D.207, A.210, K.211 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.78, A:T.85, A:L.88, A:M.140, A:W.177, A:Y.180, A:Y.180, A:Y.180, A:Y.180, A:W.184, A:A.210, A:K.211

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: F.66, G.67, K.124, V.125, Y.126 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.67, A:K.124, A:Y.126 Water bridges: A:G.68, A:G.68, A:S.127

1 x HP6: HEPTANE(Non-functional Binders)

HP6.3: 1 residues within 4Å: Ligands: D10.17 No protein-ligand interaction detected (PLIP)

8 x D12: DODECANE(Non-functional Binders)(Non-covalent)

D12.4: 2 residues within 4Å: Ligands: R16.9, D12.12 No protein-ligand interaction detected (PLIP) D12.5: 1 residues within 4Å: Ligands: D12.12 No protein-ligand interaction detected (PLIP) D12.6: 1 residues within 4Å: Ligands: D12.14 No protein-ligand interaction detected (PLIP) D12.11: 2 residues within 4Å: Chain A: I.6 Ligands: D10.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.6 D12.12: 2 residues within 4Å: Ligands: D12.4, D12.5 No protein-ligand interaction detected (PLIP) D12.14: 5 residues within 4Å: Chain A: I.193, V.194, P.195 Ligands: D12.6, D10.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.194, A:P.195 D12.15: 2 residues within 4Å: Chain A: A.105, A.139 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.105, A:A.139 D12.16: 3 residues within 4Å: Chain A: A.39, L.43 Ligands: D10.10 No protein-ligand interaction detected (PLIP)

4 x D10: DECANE(Non-covalent)

D10.7: 3 residues within 4Å: Chain A: W.5, A.9 Ligands: D12.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.5, A:A.9 D10.8: 1 residues within 4Å: Chain A: V.131 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.131 D10.10: 4 residues within 4Å: Chain A: L.20, T.50, L.53 Ligands: D12.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.20, A:T.50, A:L.53 D10.17: 4 residues within 4Å: Chain A: I.198, L.202 Ligands: HP6.3, D12.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.198, A:L.202

1 x R16: HEXADECANE(Non-covalent)

R16.9: 5 residues within 4Å: Chain A: L.141, L.144, Y.145, F.148 Ligands: D12.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.141, A:F.148

1 x DD9: nonane(Non-covalent)

DD9.13: 1 residues within 4Å: Chain A: W.132 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.132, A:W.132, A:W.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saiki, H. et al., The 1.43 angstrom crystal structure of bacteriorhodopsin crystallized from bicelles. To Be Published

Release Date

2016-02-17

Peptides

Bacteriorhodopsin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Bacteriorhodopsin