SMTL ID : 4md2.1

Ground state of bacteriorhodopsin from Halobacterium salinarum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-trimer

Ligands

54 x L2P: 2,3-DI-PHYTANYL-GLYCEROL(Non-covalent)(Non-functional Binders)

L2P.1: 2 residues within 4Å: Chain A: W.12 Ligands: L2P.6 Ligand excluded by PLIP L2P.3: 7 residues within 4Å: Chain A: L.48, I.52, T.55, M.56, F.88 Chain B: G.116 Ligands: L2P.5 Ligand excluded by PLIP L2P.4: 3 residues within 4Å: Chain A: W.80, A.84, L.123 Ligand excluded by PLIP L2P.5: 4 residues within 4Å: Chain A: Y.64, W.80 Chain B: L.123 Ligands: L2P.3 Ligand excluded by PLIP L2P.6: 3 residues within 4Å: Chain A: L.206 Ligands: L2P.1, L2P.7 Ligand excluded by PLIP L2P.7: 3 residues within 4Å: Chain A: I.198 Ligands: L2P.6, L2P.18 Ligand excluded by PLIP L2P.8: 3 residues within 4Å: Chain A: F.54, L.58 Ligands: L2P.13 Ligand excluded by PLIP L2P.9: 4 residues within 4Å: Chain A: A.184, V.188, I.191, L.207 Ligand excluded by PLIP L2P.10: 3 residues within 4Å: Chain A: L.87, P.91 Chain C: F.88 Ligand excluded by PLIP L2P.11: 4 residues within 4Å: Chain A: W.138, M.145, V.179, S.183 Ligand excluded by PLIP L2P.12: 5 residues within 4Å: Chain A: A.143, Y.147, Y.150 Chain C: M.32 Ligands: L2P.59 Ligand excluded by PLIP L2P.13: 7 residues within 4Å: Chain A: T.17, A.18, G.21, L.22, F.54, L.61 Ligands: L2P.8 Ligand excluded by PLIP L2P.14: 2 residues within 4Å: Chain A: V.173, I.222 Ligand excluded by PLIP L2P.15: 1 residues within 4Å: Chain A: W.12 Ligand excluded by PLIP L2P.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP L2P.17: 3 residues within 4Å: Chain A: W.10, I.11, A.18 Ligand excluded by PLIP L2P.18: 2 residues within 4Å: Chain A: I.198 Ligands: L2P.7 Ligand excluded by PLIP L2P.19: 14 residues within 4Å: Chain A: T.24, L.25, L.28, K.40, Y.43, A.44, T.47, A.51, F.54 Chain B: A.110, A.114, I.117, Y.147 Ligands: L2P.32 Ligand excluded by PLIP L2P.21: 2 residues within 4Å: Chain B: W.12 Ligands: L2P.26 Ligand excluded by PLIP L2P.23: 7 residues within 4Å: Chain B: L.48, I.52, T.55, M.56, F.88 Chain C: G.116 Ligands: L2P.25 Ligand excluded by PLIP L2P.24: 3 residues within 4Å: Chain B: W.80, A.84, L.123 Ligand excluded by PLIP L2P.25: 4 residues within 4Å: Chain B: Y.64, W.80 Chain C: L.123 Ligands: L2P.23 Ligand excluded by PLIP L2P.26: 3 residues within 4Å: Chain B: L.206 Ligands: L2P.21, L2P.27 Ligand excluded by PLIP L2P.27: 3 residues within 4Å: Chain B: I.198 Ligands: L2P.26, L2P.38 Ligand excluded by PLIP L2P.28: 3 residues within 4Å: Chain B: F.54, L.58 Ligands: L2P.33 Ligand excluded by PLIP L2P.29: 4 residues within 4Å: Chain B: A.184, V.188, I.191, L.207 Ligand excluded by PLIP L2P.30: 3 residues within 4Å: Chain A: F.88 Chain B: L.87, P.91 Ligand excluded by PLIP L2P.31: 4 residues within 4Å: Chain B: W.138, M.145, V.179, S.183 Ligand excluded by PLIP L2P.32: 5 residues within 4Å: Chain A: M.32 Chain B: A.143, Y.147, Y.150 Ligands: L2P.19 Ligand excluded by PLIP L2P.33: 7 residues within 4Å: Chain B: T.17, A.18, G.21, L.22, F.54, L.61 Ligands: L2P.28 Ligand excluded by PLIP L2P.34: 2 residues within 4Å: Chain B: V.173, I.222 Ligand excluded by PLIP L2P.35: 1 residues within 4Å: Chain B: W.12 Ligand excluded by PLIP L2P.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP L2P.37: 3 residues within 4Å: Chain B: W.10, I.11, A.18 Ligand excluded by PLIP L2P.38: 2 residues within 4Å: Chain B: I.198 Ligands: L2P.27 Ligand excluded by PLIP L2P.39: 14 residues within 4Å: Chain B: T.24, L.25, L.28, K.40, Y.43, A.44, T.47, A.51, F.54 Chain C: A.110, A.114, I.117, Y.147 Ligands: L2P.52 Ligand excluded by PLIP L2P.41: 2 residues within 4Å: Chain C: W.12 Ligands: L2P.46 Ligand excluded by PLIP L2P.43: 7 residues within 4Å: Chain A: G.116 Chain C: L.48, I.52, T.55, M.56, F.88 Ligands: L2P.45 Ligand excluded by PLIP L2P.44: 3 residues within 4Å: Chain C: W.80, A.84, L.123 Ligand excluded by PLIP L2P.45: 4 residues within 4Å: Chain A: L.123 Chain C: Y.64, W.80 Ligands: L2P.43 Ligand excluded by PLIP L2P.46: 3 residues within 4Å: Chain C: L.206 Ligands: L2P.41, L2P.47 Ligand excluded by PLIP L2P.47: 3 residues within 4Å: Chain C: I.198 Ligands: L2P.46, L2P.58 Ligand excluded by PLIP L2P.48: 3 residues within 4Å: Chain C: F.54, L.58 Ligands: L2P.53 Ligand excluded by PLIP L2P.49: 4 residues within 4Å: Chain C: A.184, V.188, I.191, L.207 Ligand excluded by PLIP L2P.50: 3 residues within 4Å: Chain B: F.88 Chain C: L.87, P.91 Ligand excluded by PLIP L2P.51: 4 residues within 4Å: Chain C: W.138, M.145, V.179, S.183 Ligand excluded by PLIP L2P.52: 5 residues within 4Å: Chain B: M.32 Chain C: A.143, Y.147, Y.150 Ligands: L2P.39 Ligand excluded by PLIP L2P.53: 7 residues within 4Å: Chain C: T.17, A.18, G.21, L.22, F.54, L.61 Ligands: L2P.48 Ligand excluded by PLIP L2P.54: 2 residues within 4Å: Chain C: V.173, I.222 Ligand excluded by PLIP L2P.55: 1 residues within 4Å: Chain C: W.12 Ligand excluded by PLIP L2P.56: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP L2P.57: 3 residues within 4Å: Chain C: W.10, I.11, A.18 Ligand excluded by PLIP L2P.58: 2 residues within 4Å: Chain C: I.198 Ligands: L2P.47 Ligand excluded by PLIP L2P.59: 14 residues within 4Å: Chain A: A.110, A.114, I.117, Y.147 Chain C: T.24, L.25, L.28, K.40, Y.43, A.44, T.47, A.51, F.54 Ligands: L2P.12 Ligand excluded by PLIP

3 x SQL: (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene(Non-covalent)

SQL.2: 10 residues within 4Å: Chain A: L.19, L.22, G.23, Y.26, V.213, S.214, V.217, G.218, L.221, R.225 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.19, A:L.22, A:V.217 SQL.22: 10 residues within 4Å: Chain B: L.19, L.22, G.23, Y.26, V.213, S.214, V.217, G.218, L.221, R.225 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.19, B:L.22, B:V.217 SQL.42: 10 residues within 4Å: Chain C: L.19, L.22, G.23, Y.26, V.213, S.214, V.217, G.218, L.221, R.225 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.19, C:L.22, C:V.217

3 x RET: RETINAL(Covalent)

RET.20: 15 residues within 4Å: Chain A: W.86, T.90, L.93, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.90, A:L.93, A:M.145, A:W.182, A:W.182, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:P.186, A:W.189, A:A.215, A:K.216 RET.40: 15 residues within 4Å: Chain B: W.86, T.90, L.93, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.90, B:L.93, B:M.145, B:W.182, B:W.182, B:Y.185, B:Y.185, B:Y.185, B:Y.185, B:P.186, B:W.189, B:A.215, B:K.216 RET.60: 15 residues within 4Å: Chain C: W.86, T.90, L.93, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:T.90, C:L.93, C:M.145, C:W.182, C:W.182, C:Y.185, C:Y.185, C:Y.185, C:Y.185, C:P.186, C:W.189, C:A.215, C:K.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borshchevskiy, V. et al., Low-dose X-ray radiation induces structural alterations in proteins. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-10-08

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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