SMTL ID : 3hap.1

Crystal structure of bacteriorhodopsin mutant L111A crystallized from bicelles

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x RET: RETINAL(Covalent)

RET.1: 18 residues within 4Å: Chain A: Y.83, W.86, T.90, L.93, M.118, I.119, 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:Y.83, A:T.90, A:L.93, A:I.119, A:M.145, 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:A.215, A:K.216

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

D12.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D12.3: 2 residues within 4Å: Chain A: A.139 Ligands: D12.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.139 D12.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D12.10: 4 residues within 4Å: Chain A: I.11, A.18, L.22 Ligands: D10.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.11, A:A.18, A:L.22 D12.12: 1 residues within 4Å: Ligands: D12.3 No protein-ligand interaction detected (PLIP) D12.14: 4 residues within 4Å: Chain A: I.198, V.199, P.200 Ligands: D10.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.200 D12.15: 4 residues within 4Å: Chain A: A.110, G.113, A.114, A.144 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.144 D12.16: 4 residues within 4Å: Chain A: A.44, T.47, A.51 Ligands: D10.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.44, A:T.47, A:A.51

4 x D10: DECANE(Non-covalent)

D10.5: 5 residues within 4Å: Chain A: W.10, A.14, L.61 Ligands: CPS.8, D12.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.10, A:W.10, A:A.14, A:L.61 D10.6: 3 residues within 4Å: Chain A: V.136, I.140 Ligands: DD9.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.136, A:I.140 D10.9: 4 residues within 4Å: Chain A: L.25, T.55, L.58 Ligands: D12.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.25, A:T.55, A:L.58 D10.17: 4 residues within 4Å: Chain A: L.206, L.207 Ligands: HP6.11, D12.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.206, A:L.207

1 x R16: HEXADECANE(Non-covalent)

R16.7: 3 residues within 4Å: Chain A: L.146, Y.150, F.153 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.150, A:F.153

1 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.8: 5 residues within 4Å: Chain A: G.6, W.10, L.61, L.62 Ligands: D10.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.10, A:W.10, A:L.62 Hydrogen bonds: A:G.6 Water bridges: A:W.10

1 x HP6: HEPTANE(Non-functional Binders)

HP6.11: 1 residues within 4Å: Ligands: D10.17 No protein-ligand interaction detected (PLIP)

1 x DD9: nonane(Non-covalent)

DD9.13: 3 residues within 4Å: Chain A: V.136, W.137 Ligands: D10.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joh, N.H. et al., Similar energetic contributions of packing in the core of membrane and water-soluble proteins. J.Am.Chem.Soc. (2009)

Release Date

2009-09-22

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