SMTL ID : 4pxk.1

Crystal structure of Haloarcula marismortui bacteriorhodopsin I D94N mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 15 residues within 4Å: Chain A: W.84, T.88, L.91, M.116, G.120, W.142, S.145, T.146, L.149, W.186, Y.189, P.190, W.193, D.216, K.220 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.84, A:W.84, A:T.88, A:L.91, A:L.149, A:W.186, A:Y.189, A:Y.189, A:Y.189, A:Y.189, A:P.190, A:W.193, A:W.193, A:K.220 RET.23: 15 residues within 4Å: Chain B: W.84, T.88, L.91, M.116, G.120, W.142, S.145, T.146, L.149, W.186, Y.189, P.190, W.193, D.216, K.220 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.84, B:W.84, B:T.88, B:L.91, B:L.149, B:W.186, B:Y.189, B:Y.189, B:Y.189, B:Y.189, B:P.190, B:W.193, B:W.193, B:K.220 RET.45: 15 residues within 4Å: Chain C: W.84, T.88, L.91, M.116, G.120, W.142, S.145, T.146, L.149, W.186, Y.189, P.190, W.193, D.216, K.220 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:W.84, C:W.84, C:T.88, C:L.91, C:L.149, C:W.186, C:Y.189, C:Y.189, C:Y.189, C:Y.189, C:P.190, C:W.193, C:W.193, C:K.220

57 x LFA: EICOSANE(Non-covalent)(Non-functional Binders)

LFA.2: 3 residues within 4Å: Chain A: W.78 Ligands: LFA.3, LFA.15 Ligand excluded by PLIP LFA.3: 9 residues within 4Å: Chain A: V.53, N.54, W.78, T.82 Chain C: V.122, L.125 Ligands: LFA.2, LFA.14, LFA.15 Ligand excluded by PLIP LFA.4: 2 residues within 4Å: Chain A: L.200 Ligands: LFA.13 Ligand excluded by PLIP LFA.5: 2 residues within 4Å: Chain A: L.202 Ligands: LFA.17 Ligand excluded by PLIP LFA.6: 2 residues within 4Å: Chain A: L.20, Y.24 Ligand excluded by PLIP LFA.7: 4 residues within 4Å: Chain A: L.85, P.89, L.90 Ligands: LFA.20 Ligand excluded by PLIP LFA.8: 4 residues within 4Å: Chain A: W.12 Chain C: V.131, L.132 Ligands: LFA.9 Ligand excluded by PLIP LFA.9: 3 residues within 4Å: Chain A: W.12 Ligands: LFA.8, LFA.10 Ligand excluded by PLIP LFA.10: 4 residues within 4Å: Chain A: I.9, W.12, L.13 Ligands: LFA.9 Ligand excluded by PLIP LFA.11: 4 residues within 4Å: Chain A: L.132, S.133, A.136 Ligands: LFA.12 Ligand excluded by PLIP LFA.12: 2 residues within 4Å: Ligands: LFA.11, LFA.13 Ligand excluded by PLIP LFA.13: 5 residues within 4Å: Chain A: L.139, W.142, L.194 Ligands: LFA.4, LFA.12 Ligand excluded by PLIP LFA.14: 5 residues within 4Å: Chain A: N.54, F.86 Chain C: V.114, L.115 Ligands: LFA.3 Ligand excluded by PLIP LFA.15: 4 residues within 4Å: Ligands: LFA.2, LFA.3, LFA.37, LFA.59 Ligand excluded by PLIP LFA.16: 3 residues within 4Å: Chain A: L.90, Y.93 Chain C: Y.107 Ligand excluded by PLIP LFA.17: 2 residues within 4Å: Chain A: W.192 Ligands: LFA.5 Ligand excluded by PLIP LFA.20: 6 residues within 4Å: Chain A: Y.93, A.101, R.103, I.106, Y.107 Ligands: LFA.7 Ligand excluded by PLIP LFA.21: 2 residues within 4Å: Chain A: L.20, Y.24 Ligand excluded by PLIP LFA.22: 8 residues within 4Å: Chain A: M.22, I.45, A.49 Chain C: L.112, L.115, A.147, F.148, F.155 Ligand excluded by PLIP LFA.24: 3 residues within 4Å: Chain B: W.78 Ligands: LFA.25, LFA.37 Ligand excluded by PLIP LFA.25: 9 residues within 4Å: Chain A: V.122, L.125 Chain B: V.53, N.54, W.78, T.82 Ligands: LFA.24, LFA.36, LFA.37 Ligand excluded by PLIP LFA.26: 2 residues within 4Å: Chain B: L.200 Ligands: LFA.35 Ligand excluded by PLIP LFA.27: 2 residues within 4Å: Chain B: L.202 Ligands: LFA.39 Ligand excluded by PLIP LFA.28: 2 residues within 4Å: Chain B: L.20, Y.24 Ligand excluded by PLIP LFA.29: 4 residues within 4Å: Chain B: L.85, P.89, L.90 Ligands: LFA.42 Ligand excluded by PLIP LFA.30: 4 residues within 4Å: Chain A: V.131, L.132 Chain B: W.12 Ligands: LFA.31 Ligand excluded by PLIP LFA.31: 3 residues within 4Å: Chain B: W.12 Ligands: LFA.30, LFA.32 Ligand excluded by PLIP LFA.32: 4 residues within 4Å: Chain B: I.9, W.12, L.13 Ligands: LFA.31 Ligand excluded by PLIP LFA.33: 4 residues within 4Å: Chain B: L.132, S.133, A.136 Ligands: LFA.34 Ligand excluded by PLIP LFA.34: 2 residues within 4Å: Ligands: LFA.33, LFA.35 Ligand excluded by PLIP LFA.35: 5 residues within 4Å: Chain B: L.139, W.142, L.194 Ligands: LFA.26, LFA.34 Ligand excluded by PLIP LFA.36: 5 residues within 4Å: Chain A: V.114, L.115 Chain B: N.54, F.86 Ligands: LFA.25 Ligand excluded by PLIP LFA.37: 4 residues within 4Å: Ligands: LFA.15, LFA.24, LFA.25, LFA.59 Ligand excluded by PLIP LFA.38: 3 residues within 4Å: Chain A: Y.107 Chain B: L.90, Y.93 Ligand excluded by PLIP LFA.39: 2 residues within 4Å: Chain B: W.192 Ligands: LFA.27 Ligand excluded by PLIP LFA.42: 6 residues within 4Å: Chain B: Y.93, A.101, R.103, I.106, Y.107 Ligands: LFA.29 Ligand excluded by PLIP LFA.43: 2 residues within 4Å: Chain B: L.20, Y.24 Ligand excluded by PLIP LFA.44: 8 residues within 4Å: Chain A: L.112, L.115, A.147, F.148, F.155 Chain B: M.22, I.45, A.49 Ligand excluded by PLIP LFA.46: 3 residues within 4Å: Chain C: W.78 Ligands: LFA.47, LFA.59 Ligand excluded by PLIP LFA.47: 9 residues within 4Å: Chain B: V.122, L.125 Chain C: V.53, N.54, W.78, T.82 Ligands: LFA.46, LFA.58, LFA.59 Ligand excluded by PLIP LFA.48: 2 residues within 4Å: Chain C: L.200 Ligands: LFA.57 Ligand excluded by PLIP LFA.49: 2 residues within 4Å: Chain C: L.202 Ligands: LFA.61 Ligand excluded by PLIP LFA.50: 2 residues within 4Å: Chain C: L.20, Y.24 Ligand excluded by PLIP LFA.51: 4 residues within 4Å: Chain C: L.85, P.89, L.90 Ligands: LFA.64 Ligand excluded by PLIP LFA.52: 4 residues within 4Å: Chain B: V.131, L.132 Chain C: W.12 Ligands: LFA.53 Ligand excluded by PLIP LFA.53: 3 residues within 4Å: Chain C: W.12 Ligands: LFA.52, LFA.54 Ligand excluded by PLIP LFA.54: 4 residues within 4Å: Chain C: I.9, W.12, L.13 Ligands: LFA.53 Ligand excluded by PLIP LFA.55: 4 residues within 4Å: Chain C: L.132, S.133, A.136 Ligands: LFA.56 Ligand excluded by PLIP LFA.56: 2 residues within 4Å: Ligands: LFA.55, LFA.57 Ligand excluded by PLIP LFA.57: 5 residues within 4Å: Chain C: L.139, W.142, L.194 Ligands: LFA.48, LFA.56 Ligand excluded by PLIP LFA.58: 5 residues within 4Å: Chain B: V.114, L.115 Chain C: N.54, F.86 Ligands: LFA.47 Ligand excluded by PLIP LFA.59: 4 residues within 4Å: Ligands: LFA.15, LFA.37, LFA.46, LFA.47 Ligand excluded by PLIP LFA.60: 3 residues within 4Å: Chain B: Y.107 Chain C: L.90, Y.93 Ligand excluded by PLIP LFA.61: 2 residues within 4Å: Chain C: W.192 Ligands: LFA.49 Ligand excluded by PLIP LFA.64: 6 residues within 4Å: Chain C: Y.93, A.101, R.103, I.106, Y.107 Ligands: LFA.51 Ligand excluded by PLIP LFA.65: 2 residues within 4Å: Chain C: L.20, Y.24 Ligand excluded by PLIP LFA.66: 8 residues within 4Å: Chain B: L.112, L.115, A.147, F.148, F.155 Chain C: M.22, I.45, A.49 Ligand excluded by PLIP

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

SO4.18: 2 residues within 4Å: Chain A: R.172, K.176 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.172, A:K.176 SO4.19: 2 residues within 4Å: Chain A: K.176, R.179 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.176, A:R.179 SO4.40: 2 residues within 4Å: Chain B: R.172, K.176 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.172, B:K.176 SO4.41: 2 residues within 4Å: Chain B: K.176, R.179 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.176, B:R.179 SO4.62: 2 residues within 4Å: Chain C: R.172, K.176 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.172, C:K.176 SO4.63: 2 residues within 4Å: Chain C: K.176, R.179 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.176, C:R.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shevchenko, V. et al., Crystal Structure of Escherichia coli-Expressed Haloarcula marismortui Bacteriorhodopsin I in the Trimeric Form. Plos One (2014)

Release Date

2014-12-17

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