SMTL ID : 3a7k.1

Crystal structure of halorhodopsin from Natronomonas pharaonis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: W.127, S.130, T.131, M.159, G.163, Y.180, S.183, C.184, F.187, W.222, Y.225, P.226, W.229, D.252, A.255, K.256 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.127, A:W.127, A:T.131, A:Y.180, A:F.187, A:F.187, A:W.222, A:Y.225, A:Y.225, A:Y.225, A:Y.225, A:P.226, A:W.229, A:W.229, A:A.255, A:K.256 RET.17: 16 residues within 4Å: Chain B: W.127, S.130, T.131, M.159, G.163, Y.180, S.183, C.184, F.187, W.222, Y.225, P.226, W.229, D.252, A.255, K.256 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.127, B:W.127, B:W.127, B:T.131, B:Y.180, B:F.187, B:W.222, B:Y.225, B:Y.225, B:Y.225, B:Y.225, B:Y.225, B:P.226, B:W.229, B:A.255, B:K.256 RET.26: 16 residues within 4Å: Chain C: W.127, S.130, T.131, I.134, M.159, G.163, Y.180, S.183, C.184, F.187, W.222, Y.225, P.226, W.229, D.252, K.256 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:W.127, C:W.127, C:T.131, C:I.134, C:Y.180, C:F.187, C:W.222, C:W.222, C:Y.225, C:Y.225, C:Y.225, C:Y.225, C:Y.225, C:P.226, C:W.229, C:K.256

3 x 22B: BACTERIORUBERIN(Non-covalent)

22B.2: 19 residues within 4Å: Chain A: L.29, A.35, Y.39, A.43, G.46, I.49, V.53, T.56, K.65, V.69, I.72 Chain C: T.151, F.155, A.185, V.189, I.193, E.197 Ligands: L3P.9, L3P.25 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:A.35, A:Y.39, A:A.43, A:I.49, A:K.65, A:V.69, A:I.72, C:F.155, C:F.155, C:I.193 22B.15: 21 residues within 4Å: Chain A: T.147, T.151, F.155, A.185, V.189, I.193, E.197 Chain B: L.29, Y.39, A.43, G.46, L.47, I.49, V.53, T.56, K.65, A.68, I.72, I.79 Ligands: L3P.7, L3P.8 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:Y.39, B:A.43, B:L.47, B:I.49, B:V.53, B:K.65, B:A.68, B:I.72, B:I.79, A:T.147, A:T.151, A:F.155, A:F.155, A:A.185, A:V.189, A:I.193 Water bridges: B:K.65 Hydrogen bonds: A:E.197 22B.24: 22 residues within 4Å: Chain B: T.147, K.148, T.151, F.155, I.182, A.185, V.189, I.193, E.197 Chain C: F.25, L.29, Y.39, A.43, G.46, I.49, T.56, K.65, V.69, I.72, V.76, I.79 Ligands: CL.20 19 PLIP interactions: 9 interactions with chain C, 10 interactions with chain B Hydrophobic interactions: C:F.25, C:Y.39, C:A.43, C:I.49, C:I.72, C:V.76, C:I.79, B:T.147, B:F.155, B:F.155, B:F.155, B:I.182, B:A.185, B:V.189, B:I.193 Hydrogen bonds: C:T.56, C:K.65, B:E.197, B:E.197

3 x L1P: 3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL(Non-covalent)

L1P.3: 17 residues within 4Å: Chain A: V.77, A.80, L.89, T.90, W.121, L.129 Chain C: S.92, L.94, W.121, L.125, I.157, V.161, L.164, L.168 Ligands: L1P.19, L1P.21, L2P.30 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:V.77, A:A.80, A:L.89, A:T.90, A:W.121, A:L.129, C:L.125, C:I.157, C:V.161, C:V.161, C:V.161, C:L.164, C:L.168 Hydrogen bonds: C:S.92 L1P.19: 18 residues within 4Å: Chain A: V.19, S.92, V.93, L.94, L.125, V.161, A.165, L.168 Chain B: V.19, A.80, L.89, T.90, W.121, L.125, T.126 Ligands: L1P.3, L3P.10, L1P.21 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:L.89, B:T.90, B:W.121, B:L.125, B:T.126, A:L.94, A:L.125, A:V.161, A:V.161, A:A.165, A:L.168, A:L.168 Hydrogen bonds: A:S.92 L1P.21: 19 residues within 4Å: Chain B: S.92, L.94, W.121, L.125, I.157, V.161, A.165, L.168 Chain C: A.80, L.89, S.92, W.121, L.125, T.126, L.129 Ligands: L1P.3, L1P.19, L2P.22, L2P.23 17 PLIP interactions: 6 interactions with chain C, 11 interactions with chain B Hydrophobic interactions: C:A.80, C:L.89, C:W.121, C:L.125, C:T.126, C:L.129, B:W.121, B:W.121, B:W.121, B:L.125, B:I.157, B:V.161, B:A.165, B:L.168, B:L.168 Hydrogen bonds: B:S.92 Water bridges: B:V.93

6 x L2P: 2,3-DI-PHYTANYL-GLYCEROL(Non-covalent)

L2P.4: 13 residues within 4Å: Chain A: A.146, F.150, I.153, T.154, I.157, A.158, V.161 Chain B: V.76, V.77, A.80 Ligands: L2P.5, L3P.10, L2P.22 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:V.77, B:A.80, A:A.146, A:F.150, A:F.150, A:F.150, A:I.153, A:I.153, A:T.154, A:I.157, A:I.157, A:A.158, A:V.161 L2P.5: 9 residues within 4Å: Chain A: P.132, M.133, L.136, L.140, I.157 Chain C: F.150 Ligands: L2P.4, L3P.10, L2P.30 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.132, A:L.136, A:L.136, A:L.140, A:I.157 L2P.22: 13 residues within 4Å: Chain A: A.146, F.150 Chain B: L.66, A.128, L.129, M.133, L.136, I.153, I.157 Ligands: L2P.4, L3P.10, L1P.21, L2P.23 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.66, B:L.129, B:L.136, B:L.136, B:I.153, B:I.157, A:F.150 L2P.23: 14 residues within 4Å: Chain B: A.146, L.149, F.150, I.153, T.154, I.157, A.158, V.161 Chain C: V.77, M.133 Ligands: L3P.10, L1P.21, L2P.22, L2P.29 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.146, B:L.149, B:F.150, B:I.153, B:I.153, B:I.157, B:I.157, B:A.158, B:V.161, C:V.77 L2P.29: 11 residues within 4Å: Chain B: F.150 Chain C: L.66, A.128, P.132, M.133, L.136, I.153, I.157 Ligands: L3P.10, L2P.23, L2P.30 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:P.132, C:L.136, C:L.136, C:I.153, C:I.157 L2P.30: 12 residues within 4Å: Chain A: L.129 Chain C: L.140, S.144, A.146, L.149, I.153, T.154, I.157 Ligands: L1P.3, L2P.5, L3P.10, L2P.29 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.140, C:A.146, C:L.149, C:L.149, C:L.149, C:I.153, C:T.154, A:L.129

9 x L3P: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE(Non-covalent)(Non-functional Binders)

L3P.6: 2 residues within 4Å: Chain A: L.195, Q.200 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.195 L3P.7: 5 residues within 4Å: Chain A: A.185, I.188, Y.192 Chain B: K.65 Ligands: 22B.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.185, A:I.188, A:Y.192 L3P.8: 6 residues within 4Å: Chain A: S.172, L.174, W.177, F.178 Chain B: F.25 Ligands: 22B.15 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.25, A:L.174, A:F.178 L3P.9: 5 residues within 4Å: Chain A: F.25, L.29 Chain C: L.174 Ligands: 22B.2, L3P.25 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.174, A:F.25, A:L.29 L3P.10: 7 residues within 4Å: Ligands: L2P.4, L2P.5, L1P.19, L2P.22, L2P.23, L2P.29, L2P.30 No protein-ligand interaction detected (PLIP) L3P.11: 6 residues within 4Å: Chain A: W.177, Y.180, C.184, F.187, I.188, L.191 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.177, A:W.177, A:F.187, A:I.188 L3P.12: 5 residues within 4Å: Chain A: P.32, L.33, S.36, W.246, V.254 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.33, A:L.33, A:W.246, A:W.246, A:W.246, A:V.254 L3P.16: 3 residues within 4Å: Chain B: Y.180, A.181, I.188 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.180 L3P.25: 6 residues within 4Å: Chain C: H.173, L.174, W.177, A.181 Ligands: 22B.2, L3P.9 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.177, C:W.177, C:A.181

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 5 residues within 4Å: Chain A: V.77, T.126, W.127, S.130, K.256 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: N.145, T.147, K.148 Chain B: P.62, K.65 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain B: S.81, T.126, W.127, S.130, K.256 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain B: N.145, T.147, K.148 Chain C: P.62, K.65 Ligands: 22B.24 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain C: S.81, T.126, W.127, S.130, K.256 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain A: P.62, K.65 Chain C: N.145, T.147, K.148 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kouyama, T. et al., Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas pharaonis. J.Mol.Biol. (2010)

Release Date

2009-12-15

Peptides

Halorhodopsin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Membrane

We predict this structure to be a membrane protein.
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Halorhodopsin

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