SMTL ID : 1vgo.1

Crystal Structure of Archaerhodopsin-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

12 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)(Non-functional Binders)

BNG.1: 3 residues within 4Å: Chain A: I.129, L.132, W.142 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.129, A:W.142 Hydrogen bonds: A:L.132 BNG.2: 6 residues within 4Å: Chain A: P.136, L.137, Y.140, T.141, L.144 Ligands: BNG.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.137, A:Y.140, A:Y.140, A:L.144 Hydrogen bonds: A:L.137 BNG.3: 4 residues within 4Å: Chain A: L.144, I.148 Ligands: BNG.2, BNG.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.144, A:I.148 BNG.4: 8 residues within 4Å: Chain A: Y.140, W.143, L.144, I.195, G.200, A.201 Ligands: BNG.3, BNG.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.140, A:Y.140, A:W.143, A:L.144, A:A.201 Hydrogen bonds: A:Y.140 BNG.5: 6 residues within 4Å: Chain A: T.147, F.150, L.151, I.195, V.196 Ligands: BNG.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.150, A:L.151 BNG.6: 4 residues within 4Å: Chain A: V.185, I.208 Ligands: BNG.7, BNG.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.185 BNG.7: 1 residues within 4Å: Ligands: BNG.6 No protein-ligand interaction detected (PLIP) BNG.8: 3 residues within 4Å: Chain A: W.16, T.219 Ligands: BNG.6 No protein-ligand interaction detected (PLIP) BNG.9: 3 residues within 4Å: Chain A: I.68, G.69, Y.85 No protein-ligand interaction detected (PLIP) BNG.12: 4 residues within 4Å: Chain B: T.115, V.119, F.145, Y.156 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.115, B:V.119 Hydrogen bonds: B:T.115 BNG.13: 4 residues within 4Å: Chain B: F.29, A.33, W.36, G.37 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.29, B:W.36 BNG.14: 11 residues within 4Å: Chain B: L.75, A.76, S.77, T.79, K.134, P.136, R.139, Y.140, I.195, G.200, A.201 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:R.139, B:Y.140, B:I.195 Hydrogen bonds: B:A.76, B:S.77, B:S.77, B:T.79, B:K.134, B:R.139

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 4 residues within 4Å: Chain A: R.168, S.169, V.172 Chain B: R.232 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.169, A:S.169 Salt bridges: A:R.168, B:R.232 SO4.15: 4 residues within 4Å: Chain A: R.232 Chain B: R.168, S.169, V.172 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.232, B:R.168 Hydrogen bonds: B:S.169 SO4.16: 4 residues within 4Å: Chain B: W.36, V.38, T.39, R.44 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.44

2 x RET: RETINAL(Covalent)

RET.11: 15 residues within 4Å: Chain A: W.91, T.94, T.95, L.98, M.123, W.143, S.146, T.147, F.150, W.187, Y.190, P.191, W.194, D.217, K.221 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.91, A:T.94, A:T.95, A:L.98, A:F.150, A:W.187, A:W.187, A:Y.190, A:Y.190, A:Y.190, A:Y.190, A:P.191, A:W.194, A:K.221 RET.17: 16 residues within 4Å: Chain B: W.91, T.94, T.95, L.98, M.123, W.143, S.146, T.147, F.150, W.187, Y.190, P.191, W.194, D.217, A.220, K.221 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.91, B:W.91, B:T.94, B:T.95, B:L.98, B:F.150, B:W.187, B:W.187, B:Y.190, B:Y.190, B:Y.190, B:P.191, B:W.194, B:A.220, B:K.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Enami, N. et al., Crystal structures of archaerhodopsin-1 and -2: Common structural motif in archaeal light-driven proton pumps. J.Mol.Biol. (2006)

Release Date

2005-10-04

Peptides

Archaerhodopsin 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Archaerhodopsin 2

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