SMTL ID : 2brd.1

CRYSTAL STRUCTURE OF BACTERIORHODOPSIN IN PURPLE MEMBRANE

Coordinates

PDB Format Compare

Method

ELECTRON CRYSTALLOGRAPHY 3.50 Å

Oligo State

homo-trimer

Ligands

30 x DPG: PHOSPHORIC ACID 2,3-BIS-(3,7,11,15-TETRAMETHYL-HEXADECYLOXY)-PROPYL ESTER 2-HYDROXO-3-PHOSPHONOOXY-PROPYL ESTER(Non-covalent)(Non-functional Binders)

DPG.1: 18 residues within 4Å: Chain A: L.66, M.68, P.70, N.76, W.80, L.87, F.88, G.120, V.124, K.129 Chain B: Y.64, L.66, W.80, F.88 Ligands: DPG.6, DPG.12, DPG.17, DPG.23 Ligand excluded by PLIP DPG.2: 7 residues within 4Å: Chain A: V.187, I.191, I.198, L.207 Ligands: DPG.3, DPG.7, DPG.8 Ligand excluded by PLIP DPG.3: 8 residues within 4Å: Chain A: W.12, I.203, L.206, V.210 Ligands: DPG.2, DPG.4, DPG.5, DPG.8 Ligand excluded by PLIP DPG.4: 2 residues within 4Å: Ligands: DPG.3, DPG.5 Ligand excluded by PLIP DPG.5: 6 residues within 4Å: Chain A: I.11, L.15, A.18, L.19 Ligands: DPG.3, DPG.4 Ligand excluded by PLIP DPG.6: 18 residues within 4Å: Chain A: F.88, L.95, Q.105, I.108, G.113, G.116, I.117 Chain B: I.52, F.88, L.92, L.99, A.103 Chain C: Q.105, L.109 Ligands: DPG.1, DPG.17, DPG.23, DPG.28 Ligand excluded by PLIP DPG.7: 10 residues within 4Å: Chain A: F.156, K.172, R.175, N.176, V.180, S.183, A.184, V.187 Ligands: DPG.2, DPG.8 Ligand excluded by PLIP DPG.8: 9 residues within 4Å: Chain A: S.169, K.172, V.173, V.210, S.214, R.225 Ligands: DPG.2, DPG.3, DPG.7 Ligand excluded by PLIP DPG.9: 12 residues within 4Å: Chain A: L.28, M.32, G.33, S.35, K.40, Y.43, A.44, T.47, A.51 Chain C: A.110, Y.147, F.154 Ligand excluded by PLIP DPG.10: 2 residues within 4Å: Chain A: L.22, V.29 Ligand excluded by PLIP DPG.12: 18 residues within 4Å: Chain B: L.66, M.68, P.70, N.76, W.80, L.87, F.88, G.120, V.124, K.129 Chain C: Y.64, L.66, W.80, F.88 Ligands: DPG.1, DPG.17, DPG.23, DPG.28 Ligand excluded by PLIP DPG.13: 7 residues within 4Å: Chain B: V.187, I.191, I.198, L.207 Ligands: DPG.14, DPG.18, DPG.19 Ligand excluded by PLIP DPG.14: 8 residues within 4Å: Chain B: W.12, I.203, L.206, V.210 Ligands: DPG.13, DPG.15, DPG.16, DPG.19 Ligand excluded by PLIP DPG.15: 2 residues within 4Å: Ligands: DPG.14, DPG.16 Ligand excluded by PLIP DPG.16: 6 residues within 4Å: Chain B: I.11, L.15, A.18, L.19 Ligands: DPG.14, DPG.15 Ligand excluded by PLIP DPG.17: 18 residues within 4Å: Chain A: Q.105, L.109 Chain B: F.88, L.95, Q.105, I.108, G.113, G.116, I.117 Chain C: I.52, F.88, L.92, L.99, A.103 Ligands: DPG.1, DPG.6, DPG.12, DPG.28 Ligand excluded by PLIP DPG.18: 10 residues within 4Å: Chain B: F.156, K.172, R.175, N.176, V.180, S.183, A.184, V.187 Ligands: DPG.13, DPG.19 Ligand excluded by PLIP DPG.19: 9 residues within 4Å: Chain B: S.169, K.172, V.173, V.210, S.214, R.225 Ligands: DPG.13, DPG.14, DPG.18 Ligand excluded by PLIP DPG.20: 12 residues within 4Å: Chain A: A.110, Y.147, F.154 Chain B: L.28, M.32, G.33, S.35, K.40, Y.43, A.44, T.47, A.51 Ligand excluded by PLIP DPG.21: 2 residues within 4Å: Chain B: L.22, V.29 Ligand excluded by PLIP DPG.23: 18 residues within 4Å: Chain A: Y.64, L.66, W.80, F.88 Chain C: L.66, M.68, P.70, N.76, W.80, L.87, F.88, G.120, V.124, K.129 Ligands: DPG.1, DPG.6, DPG.12, DPG.28 Ligand excluded by PLIP DPG.24: 7 residues within 4Å: Chain C: V.187, I.191, I.198, L.207 Ligands: DPG.25, DPG.29, DPG.30 Ligand excluded by PLIP DPG.25: 8 residues within 4Å: Chain C: W.12, I.203, L.206, V.210 Ligands: DPG.24, DPG.26, DPG.27, DPG.30 Ligand excluded by PLIP DPG.26: 2 residues within 4Å: Ligands: DPG.25, DPG.27 Ligand excluded by PLIP DPG.27: 6 residues within 4Å: Chain C: I.11, L.15, A.18, L.19 Ligands: DPG.25, DPG.26 Ligand excluded by PLIP DPG.28: 18 residues within 4Å: Chain A: I.52, F.88, L.92, L.99, A.103 Chain B: Q.105, L.109 Chain C: F.88, L.95, Q.105, I.108, G.113, G.116, I.117 Ligands: DPG.6, DPG.12, DPG.17, DPG.23 Ligand excluded by PLIP DPG.29: 10 residues within 4Å: Chain C: F.156, K.172, R.175, N.176, V.180, S.183, A.184, V.187 Ligands: DPG.24, DPG.30 Ligand excluded by PLIP DPG.30: 9 residues within 4Å: Chain C: S.169, K.172, V.173, V.210, S.214, R.225 Ligands: DPG.24, DPG.25, DPG.29 Ligand excluded by PLIP DPG.31: 12 residues within 4Å: Chain B: A.110, Y.147, F.154 Chain C: L.28, M.32, G.33, S.35, K.40, Y.43, A.44, T.47, A.51 Ligand excluded by PLIP DPG.32: 2 residues within 4Å: Chain C: L.22, V.29 Ligand excluded by PLIP

3 x RET: RETINAL(Covalent)

RET.11: 13 residues within 4Å: Chain A: W.86, T.89, T.90, M.118, W.138, S.141, M.145, W.182, Y.185, P.186, W.189, D.212, K.216 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.86, A:T.89, A:M.145, A:Y.185, A:Y.185, A:Y.185, A:P.186, A:W.189, A:K.216 RET.22: 13 residues within 4Å: Chain B: W.86, T.89, T.90, M.118, W.138, S.141, M.145, W.182, Y.185, P.186, W.189, D.212, K.216 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.86, B:T.89, B:M.145, B:Y.185, B:Y.185, B:Y.185, B:P.186, B:W.189, B:K.216 RET.33: 13 residues within 4Å: Chain C: W.86, T.89, T.90, M.118, W.138, S.141, M.145, W.182, Y.185, P.186, W.189, D.212, K.216 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.86, C:T.89, C:M.145, C:Y.185, C:Y.185, C:Y.185, C:P.186, C:W.189, C:K.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grigorieff, N. et al., Electron-crystallographic refinement of the structure of bacteriorhodopsin. J.Mol.Biol. (1996)

Release Date

1996-06-10

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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