SMTL ID : 4jq6.1

Crystal structure of blue light-absorbing proteorhodopsin from Med12 at 2.3 Angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-hexamer

Ligands

6 x RET: RETINAL(Covalent)

RET.1: 17 residues within 4Å: Chain A: Y.77, W.80, T.83, V.84, Q.87, M.116, G.120, W.134, G.137, M.138, W.141, W.180, Y.183, P.184, Y.187, D.209, K.213 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.80, A:V.84, A:W.141, A:W.180, A:Y.183, A:Y.183, A:Y.187, A:K.213 RET.2: 17 residues within 4Å: Chain B: Y.77, W.80, T.83, V.84, Q.87, M.116, G.120, W.134, G.137, M.138, W.141, W.180, Y.183, Y.187, Y.205, D.209, K.213 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.80, B:V.84, B:W.141, B:W.180, B:Y.183, B:Y.183, B:Y.187, B:K.213 RET.5: 17 residues within 4Å: Chain C: Y.77, W.80, T.83, V.84, Q.87, M.116, G.120, W.134, G.137, M.138, W.141, W.180, Y.183, P.184, Y.187, D.209, K.213 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.80, C:V.84, C:W.141, C:W.180, C:Y.183, C:Y.183, C:Y.183, C:Y.183, C:P.184, C:Y.187, C:K.213 RET.6: 17 residues within 4Å: Chain D: Y.77, W.80, T.83, V.84, Q.87, M.116, G.120, W.134, G.137, M.138, W.141, W.180, Y.183, P.184, Y.187, D.209, K.213 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:W.80, D:V.84, D:W.141, D:W.180, D:Y.183, D:Y.183, D:Y.187, D:K.213 RET.7: 17 residues within 4Å: Chain E: Y.77, W.80, T.83, V.84, Q.87, M.116, G.120, W.134, G.137, M.138, W.141, W.180, Y.183, Y.187, Y.205, D.209, K.213 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:W.80, E:V.84, E:W.141, E:W.180, E:Y.183, E:Y.183, E:Y.187, E:K.213 RET.10: 17 residues within 4Å: Chain F: Y.77, W.80, T.83, V.84, Q.87, M.116, G.120, W.134, G.137, M.138, W.141, W.180, Y.183, P.184, Y.187, D.209, K.213 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:W.80, F:V.84, F:W.141, F:W.180, F:Y.183, F:Y.183, F:Y.183, F:Y.183, F:P.184, F:Y.187, F:K.213

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

LI1.3: 5 residues within 4Å: Chain A: V.31, S.34 Chain B: F.30, R.33, S.34 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.30, A:V.31 LI1.4: 2 residues within 4Å: Chain B: A.200, V.204 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.204 LI1.8: 5 residues within 4Å: Chain D: V.31, S.34 Chain E: F.30, R.33, S.34 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:V.31, E:F.30 LI1.9: 2 residues within 4Å: Chain E: A.200, V.204 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ran, T. et al., Cross-protomer interaction with the photoactive site in oligomeric proteorhodopsin complexes. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-05-08

Peptides

Proteorhodopsin: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Membrane

We predict this structure to be a membrane protein.
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Proteorhodopsin