SMTL ID : 1m0k.1

BACTERIORHODOPSIN K INTERMEDIATE AT 1.43 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: W.99, T.102, T.103, L.106, M.131, W.151, S.154, T.155, M.158, W.195, Y.198, P.199, W.202, D.225, A.228, K.229 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.103, A:L.106, A:M.158, A:W.195, A:W.195, A:Y.198, A:Y.198, A:Y.198, A:P.199, A:W.202, A:A.228, A:K.229 RET.16: 16 residues within 4Å: Chain B: W.99, T.102, T.103, L.106, M.131, W.151, S.154, T.155, M.158, W.195, Y.198, P.199, W.202, D.225, A.228, K.229 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.103, B:L.106, B:M.158, B:W.195, B:W.195, B:Y.198, B:Y.198, B:Y.198, B:P.199, B:W.202, B:A.228, B:K.229 RET.31: 16 residues within 4Å: Chain C: W.99, T.102, T.103, L.106, M.131, W.151, S.154, T.155, M.158, W.195, Y.198, P.199, W.202, D.225, A.228, K.229 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:T.103, C:L.106, C:M.158, C:W.195, C:W.195, C:Y.198, C:Y.198, C:Y.198, C:P.199, C:W.202, C:A.228, C:K.229

39 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: 8 residues within 4Å: Chain A: Y.146, V.149, I.153, A.156 Chain B: L.71 Ligands: LI1.3, LI1.9, LI1.22 Ligand excluded by PLIP LI1.3: 10 residues within 4Å: Chain A: Y.144, F.148, V.149, W.151, A.152, L.203, A.209 Ligands: LI1.2, LI1.4, LI1.9 Ligand excluded by PLIP LI1.4: 3 residues within 4Å: Chain A: L.203, I.211 Ligands: LI1.3 Ligand excluded by PLIP LI1.5: 2 residues within 4Å: Chain A: I.211 Ligands: LI1.11 Ligand excluded by PLIP LI1.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LI1.7: 6 residues within 4Å: Chain A: A.27, T.30, A.31, L.35 Ligands: LI1.12, LI1.32 Ligand excluded by PLIP LI1.8: 13 residues within 4Å: Chain A: T.68, M.69, Y.77, W.93, F.101 Chain C: W.93, A.97, F.101, G.129, I.130, L.140 Ligands: LI1.23, LI1.38 Ligand excluded by PLIP LI1.9: 4 residues within 4Å: Chain A: A.152, A.156 Ligands: LI1.2, LI1.3 Ligand excluded by PLIP LI1.10: 1 residues within 4Å: Chain A: F.167 Ligand excluded by PLIP LI1.11: 9 residues within 4Å: Chain A: F.166, K.185, R.188, N.189, V.192, V.193, S.196, V.200 Ligands: LI1.5 Ligand excluded by PLIP LI1.12: 5 residues within 4Å: Chain A: L.35, L.38, Y.39, V.42 Ligands: LI1.7 Ligand excluded by PLIP LI1.13: 12 residues within 4Å: Chain A: T.37, L.38, L.41, Y.56, A.57, T.60, L.61, F.67 Chain C: A.123, A.127, A.157, Y.160 Ligand excluded by PLIP LI1.14: 6 residues within 4Å: Chain A: L.100, F.101, P.104, L.105, L.108, V.125 Ligand excluded by PLIP LI1.17: 8 residues within 4Å: Chain B: Y.146, V.149, I.153, A.156 Chain C: L.71 Ligands: LI1.18, LI1.24, LI1.37 Ligand excluded by PLIP LI1.18: 10 residues within 4Å: Chain B: Y.144, F.148, V.149, W.151, A.152, L.203, A.209 Ligands: LI1.17, LI1.19, LI1.24 Ligand excluded by PLIP LI1.19: 3 residues within 4Å: Chain B: L.203, I.211 Ligands: LI1.18 Ligand excluded by PLIP LI1.20: 2 residues within 4Å: Chain B: I.211 Ligands: LI1.26 Ligand excluded by PLIP LI1.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LI1.22: 6 residues within 4Å: Chain B: A.27, T.30, A.31, L.35 Ligands: LI1.2, LI1.27 Ligand excluded by PLIP LI1.23: 13 residues within 4Å: Chain A: W.93, A.97, F.101, G.129, I.130, L.140 Chain B: T.68, M.69, Y.77, W.93, F.101 Ligands: LI1.8, LI1.38 Ligand excluded by PLIP LI1.24: 4 residues within 4Å: Chain B: A.152, A.156 Ligands: LI1.17, LI1.18 Ligand excluded by PLIP LI1.25: 1 residues within 4Å: Chain B: F.167 Ligand excluded by PLIP LI1.26: 9 residues within 4Å: Chain B: F.166, K.185, R.188, N.189, V.192, V.193, S.196, V.200 Ligands: LI1.20 Ligand excluded by PLIP LI1.27: 5 residues within 4Å: Chain B: L.35, L.38, Y.39, V.42 Ligands: LI1.22 Ligand excluded by PLIP LI1.28: 12 residues within 4Å: Chain A: A.123, A.127, A.157, Y.160 Chain B: T.37, L.38, L.41, Y.56, A.57, T.60, L.61, F.67 Ligand excluded by PLIP LI1.29: 6 residues within 4Å: Chain B: L.100, F.101, P.104, L.105, L.108, V.125 Ligand excluded by PLIP LI1.32: 8 residues within 4Å: Chain A: L.71 Chain C: Y.146, V.149, I.153, A.156 Ligands: LI1.7, LI1.33, LI1.39 Ligand excluded by PLIP LI1.33: 10 residues within 4Å: Chain C: Y.144, F.148, V.149, W.151, A.152, L.203, A.209 Ligands: LI1.32, LI1.34, LI1.39 Ligand excluded by PLIP LI1.34: 3 residues within 4Å: Chain C: L.203, I.211 Ligands: LI1.33 Ligand excluded by PLIP LI1.35: 2 residues within 4Å: Chain C: I.211 Ligands: LI1.41 Ligand excluded by PLIP LI1.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LI1.37: 6 residues within 4Å: Chain C: A.27, T.30, A.31, L.35 Ligands: LI1.17, LI1.42 Ligand excluded by PLIP LI1.38: 13 residues within 4Å: Chain B: W.93, A.97, F.101, G.129, I.130, L.140 Chain C: T.68, M.69, Y.77, W.93, F.101 Ligands: LI1.8, LI1.23 Ligand excluded by PLIP LI1.39: 4 residues within 4Å: Chain C: A.152, A.156 Ligands: LI1.32, LI1.33 Ligand excluded by PLIP LI1.40: 1 residues within 4Å: Chain C: F.167 Ligand excluded by PLIP LI1.41: 9 residues within 4Å: Chain C: F.166, K.185, R.188, N.189, V.192, V.193, S.196, V.200 Ligands: LI1.35 Ligand excluded by PLIP LI1.42: 5 residues within 4Å: Chain C: L.35, L.38, Y.39, V.42 Ligands: LI1.37 Ligand excluded by PLIP LI1.43: 12 residues within 4Å: Chain B: A.123, A.127, A.157, Y.160 Chain C: T.37, L.38, L.41, Y.56, A.57, T.60, L.61, F.67 Ligand excluded by PLIP LI1.44: 6 residues within 4Å: Chain C: L.100, F.101, P.104, L.105, L.108, V.125 Ligand excluded by PLIP

3 x SQU: 2,10,23-TRIMETHYL-TETRACOSANE(Non-covalent)

SQU.15: 6 residues within 4Å: Chain A: L.32, V.226, S.227, V.230, G.231, L.234 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.32, A:V.226, A:V.230, A:L.234 SQU.30: 6 residues within 4Å: Chain B: L.32, V.226, S.227, V.230, G.231, L.234 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.32, B:V.226, B:V.230, B:L.234 SQU.45: 6 residues within 4Å: Chain C: L.32, V.226, S.227, V.230, G.231, L.234 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.32, C:V.226, C:V.230, C:L.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schobert, B. et al., Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal. J.Mol.Biol. (2002)

Release Date

2002-09-11

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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