SMTL ID : 7vso.1

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with HAD16 Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x RET: RETINAL(Covalent)

RET.1: 17 residues within 4Å: Chain A: Y.83, W.86, T.89, 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 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.83, A:W.86, A:T.90, A:L.93, A:M.145, A:W.182, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:P.186, A:P.186, A:W.189, A:A.215, A:K.216 RET.21: 17 residues within 4Å: Chain B: Y.83, W.86, T.89, 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 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.83, B:W.86, B:T.90, B:L.93, B:M.145, B:W.182, B:Y.185, B:Y.185, B:Y.185, B:Y.185, B:Y.185, B:P.186, B:P.186, B:W.189, B:A.215, B:K.216

2 x 7YH: 2-[[(2R)-2-(3-bromanyl-5-iodanyl-phenyl)carbonyloxy-3-tetradecanoyloxy-propoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium(Non-covalent)

7YH.2: 5 residues within 4Å: Chain A: L.22, Y.26, K.30 Ligands: D10.12, HP6.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.26 Hydrogen bonds: A:Y.26 Salt bridges: A:K.30 pi-Stacking: A:Y.26 7YH.22: 5 residues within 4Å: Chain B: L.22, Y.26, K.30 Ligands: D10.32, HP6.34 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.26 Salt bridges: B:K.30 pi-Stacking: B:Y.26

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 1 residues within 4Å: Ligands: OCT.5 Ligand excluded by PLIP IOD.23: 1 residues within 4Å: Ligands: OCT.25 Ligand excluded by PLIP

2 x CPS: 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE(Non-covalent)

CPS.4: 4 residues within 4Å: Chain A: R.7, W.10, L.61, L.62 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.10, A:L.61 Hydrogen bonds: A:R.7 CPS.24: 4 residues within 4Å: Chain B: R.7, W.10, L.61, L.62 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.10, B:L.61 Hydrogen bonds: B:R.7

4 x OCT: N-OCTANE(Non-covalent)

OCT.5: 2 residues within 4Å: Chain A: R.225 Ligands: IOD.3 No protein-ligand interaction detected (PLIP) OCT.20: 1 residues within 4Å: Chain A: V.124 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.124 OCT.25: 2 residues within 4Å: Chain B: R.225 Ligands: IOD.23 No protein-ligand interaction detected (PLIP) OCT.40: 1 residues within 4Å: Chain B: V.124 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.124

10 x HP6: HEPTANE(Non-functional Binders)(Non-covalent)

HP6.6: 1 residues within 4Å: Ligands: R16.8 No protein-ligand interaction detected (PLIP) HP6.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.13: 2 residues within 4Å: Chain A: L.206, L.207 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.206, A:L.207 HP6.14: 2 residues within 4Å: Ligands: 7YH.2, R16.18 No protein-ligand interaction detected (PLIP) HP6.19: 1 residues within 4Å: Ligands: D10.29 No protein-ligand interaction detected (PLIP) HP6.26: 1 residues within 4Å: Ligands: R16.28 No protein-ligand interaction detected (PLIP) HP6.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HP6.33: 2 residues within 4Å: Chain B: L.206, L.207 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.206, B:L.207 HP6.34: 2 residues within 4Å: Ligands: 7YH.22, R16.38 No protein-ligand interaction detected (PLIP) HP6.39: 1 residues within 4Å: Ligands: D10.9 No protein-ligand interaction detected (PLIP)

6 x D12: DODECANE(Non-covalent)

D12.7: 4 residues within 4Å: Chain A: G.31, M.32, K.40, A.44 No protein-ligand interaction detected (PLIP) D12.16: 3 residues within 4Å: Chain A: A.110, A.144, Y.147 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.110 D12.17: 3 residues within 4Å: Chain A: V.199 Ligands: R16.28, D12.37 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.199 D12.27: 4 residues within 4Å: Chain B: G.31, M.32, K.40, A.44 No protein-ligand interaction detected (PLIP) D12.36: 3 residues within 4Å: Chain B: A.110, A.144, Y.147 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.110 D12.37: 3 residues within 4Å: Chain B: V.199 Ligands: R16.8, D12.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.199

6 x R16: HEXADECANE(Non-covalent)

R16.8: 5 residues within 4Å: Chain A: N.176, L.181 Chain B: I.198 Ligands: HP6.6, D12.37 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.198, A:N.176 R16.10: 7 residues within 4Å: Chain A: F.153 Chain B: S.132, F.135, V.136, L.190, A.196 Ligands: D10.9 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.135, B:V.136, B:L.190, B:A.196, A:F.153 R16.18: 4 residues within 4Å: Chain A: W.10, I.11, A.18 Ligands: HP6.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.10, A:W.10, A:I.11, A:A.18 R16.28: 5 residues within 4Å: Chain A: I.198 Chain B: N.176, L.181 Ligands: D12.17, HP6.26 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.176, A:I.198 R16.30: 7 residues within 4Å: Chain A: S.132, F.135, V.136, L.190, A.196 Chain B: F.153 Ligands: D10.29 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.135, A:V.136, A:L.190, A:A.196, B:F.153 R16.38: 4 residues within 4Å: Chain B: W.10, I.11, A.18 Ligands: HP6.34 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.10, B:W.10, B:I.11, B:A.18

4 x D10: DECANE(Non-covalent)(Non-functional Binders)

D10.9: 5 residues within 4Å: Chain A: A.143, Y.147, Y.150 Ligands: R16.10, HP6.39 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.143, A:Y.147, A:Y.150 D10.12: 1 residues within 4Å: Ligands: 7YH.2 No protein-ligand interaction detected (PLIP) D10.29: 5 residues within 4Å: Chain B: A.143, Y.147, Y.150 Ligands: HP6.19, R16.30 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.143, B:Y.147, B:Y.150 D10.32: 1 residues within 4Å: Ligands: 7YH.22 No protein-ligand interaction detected (PLIP)

2 x DD9: nonane(Non-covalent)

DD9.15: 1 residues within 4Å: Chain A: W.137 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.137, A:W.137 DD9.35: 1 residues within 4Å: Chain B: W.137 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.137, B:W.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hanashima, S. et al., Heavy Atom Detergent/Lipid Combined X-ray Crystallography for Elucidating the Structure-Function Relationships of Membrane Proteins. Membranes (Basel) (2021)

Release Date

2022-02-16

Peptides

Bacteriorhodopsin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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Bacteriorhodopsin

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