SMTL ID : 4xtn.1 (1 other biounit)

Crystal structure of the light-driven sodium pump KR2 in the pentameric red form, pH 4.9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-pentamer

Ligands

5 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: Y.25, T.83, F.86, T.87 Chain B: D.102 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.102 Water bridges: B:D.102 NA.14: 4 residues within 4Å: Chain B: Y.25, T.83, F.86 Chain C: D.102 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.102 Water bridges: C:D.102 NA.26: 4 residues within 4Å: Chain C: Y.25, T.83, F.86 Chain D: D.102 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.102 NA.39: 4 residues within 4Å: Chain D: Y.25, T.83, F.86 Chain E: D.102 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.102 Water bridges: E:D.102 NA.57: 4 residues within 4Å: Chain A: D.102 Chain E: Y.25, T.83, F.86 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Water bridges: E:Y.25, A:D.102 Hydrogen bonds: A:D.102

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

LFA.2: 3 residues within 4Å: Chain A: P.118, W.143 Chain E: V.260 Ligand excluded by PLIP LFA.3: 3 residues within 4Å: Chain A: N.140, W.143 Ligands: LFA.63 Ligand excluded by PLIP LFA.4: 4 residues within 4Å: Chain A: N.163, T.165, V.169, W.170 Ligand excluded by PLIP LFA.5: 4 residues within 4Å: Chain A: S.145, A.176, F.177, H.180 Ligand excluded by PLIP LFA.6: 7 residues within 4Å: Chain A: L.40, L.44, I.47, L.48 Chain B: L.43 Ligands: LFA.15, LFA.16 Ligand excluded by PLIP LFA.7: 9 residues within 4Å: Chain A: V.38, Y.45, V.256, N.264 Chain B: L.63, V.66, M.119, F.122, F.126 Ligand excluded by PLIP LFA.8: 2 residues within 4Å: Chain B: R.139 Ligands: LFA.9 Ligand excluded by PLIP LFA.9: 6 residues within 4Å: Chain A: N.206, I.209, L.210, I.213, S.253 Ligands: LFA.8 Ligand excluded by PLIP LFA.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LFA.11: 6 residues within 4Å: Chain A: Y.76 Chain E: F.72, Y.76 Ligands: LFA.40, LFA.44, LFA.58 Ligand excluded by PLIP LFA.12: 5 residues within 4Å: Chain A: L.168, G.171, A.172, S.175, L.223 Ligand excluded by PLIP LFA.15: 5 residues within 4Å: Chain A: F.72 Chain B: L.73, Y.76 Ligands: LFA.6, LFA.58 Ligand excluded by PLIP LFA.16: 4 residues within 4Å: Chain C: L.73 Ligands: LFA.6, LFA.20, LFA.27 Ligand excluded by PLIP LFA.17: 4 residues within 4Å: Chain A: I.257 Chain B: R.139, W.143 Ligands: LFA.18 Ligand excluded by PLIP LFA.18: 2 residues within 4Å: Chain B: F.144 Ligands: LFA.17 Ligand excluded by PLIP LFA.19: 4 residues within 4Å: Chain B: N.163, A.166, V.169 Ligands: MPG.25 Ligand excluded by PLIP LFA.20: 6 residues within 4Å: Chain B: L.44, I.47, L.48 Chain C: I.47 Ligands: LFA.16, LFA.27 Ligand excluded by PLIP LFA.21: 9 residues within 4Å: Chain B: Y.45, V.260, N.264 Chain C: V.66, L.114, I.115, M.119, F.122 Ligands: LFA.22 Ligand excluded by PLIP LFA.22: 8 residues within 4Å: Chain B: I.257, V.260, N.264 Chain C: P.118, M.119, R.139, W.143 Ligands: LFA.21 Ligand excluded by PLIP LFA.23: 7 residues within 4Å: Chain B: L.210, I.213, L.217, V.246, I.249, S.253 Ligands: LFA.24 Ligand excluded by PLIP LFA.24: 2 residues within 4Å: Ligands: LFA.23, LFA.29 Ligand excluded by PLIP LFA.27: 8 residues within 4Å: Chain C: L.40, F.72 Chain D: L.73, Y.76 Ligands: LFA.16, LFA.20, LFA.31, LFA.40 Ligand excluded by PLIP LFA.28: 1 residues within 4Å: Chain C: R.139 Ligand excluded by PLIP LFA.29: 2 residues within 4Å: Chain C: F.144 Ligands: LFA.24 Ligand excluded by PLIP LFA.30: 6 residues within 4Å: Chain C: N.163, T.165, A.166, V.169, W.170, I.173 Ligand excluded by PLIP LFA.31: 7 residues within 4Å: Chain C: L.44, I.47, L.48 Chain D: L.43, I.47 Ligands: LFA.27, LFA.40 Ligand excluded by PLIP LFA.32: 8 residues within 4Å: Chain C: V.38, Y.45, V.260, N.264 Chain D: V.66, L.114, I.115, F.122 Ligand excluded by PLIP LFA.33: 2 residues within 4Å: Chain C: N.206 Ligands: LFA.41 Ligand excluded by PLIP LFA.34: 3 residues within 4Å: Chain C: N.206, L.210, S.253 Ligand excluded by PLIP LFA.35: 2 residues within 4Å: Chain C: V.246, I.249 Ligand excluded by PLIP LFA.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LFA.37: 4 residues within 4Å: Chain C: L.168, G.171, S.175, L.223 Ligand excluded by PLIP LFA.40: 8 residues within 4Å: Chain D: F.72, Y.76 Chain E: L.73, Y.76 Ligands: LFA.11, LFA.27, LFA.31, LFA.67 Ligand excluded by PLIP LFA.41: 5 residues within 4Å: Chain C: V.260, N.264 Chain D: P.118, R.139 Ligands: LFA.33 Ligand excluded by PLIP LFA.42: 3 residues within 4Å: Chain D: N.140, F.144, A.147 Ligand excluded by PLIP LFA.43: 5 residues within 4Å: Chain D: N.163, T.165, V.169, W.170, I.173 Ligand excluded by PLIP LFA.44: 7 residues within 4Å: Chain D: L.40, L.44, I.47, L.48 Chain E: L.43, I.47 Ligands: LFA.11 Ligand excluded by PLIP LFA.45: 12 residues within 4Å: Chain D: V.38, Y.45, V.256, V.260, L.275 Chain E: V.66, L.114, I.115, F.122, F.126 Ligands: LFA.46, LFA.64 Ligand excluded by PLIP LFA.46: 2 residues within 4Å: Chain D: I.257 Ligands: LFA.45 Ligand excluded by PLIP LFA.47: 4 residues within 4Å: Chain D: N.206, L.210, I.213, S.253 Ligand excluded by PLIP LFA.48: 1 residues within 4Å: Ligands: LFA.65 Ligand excluded by PLIP LFA.49: 1 residues within 4Å: Chain D: Y.226 Ligand excluded by PLIP LFA.50: 6 residues within 4Å: Chain D: L.168, G.171, A.172, S.175, Y.222, L.223 Ligand excluded by PLIP LFA.51: 2 residues within 4Å: Chain D: A.176, F.177 Ligand excluded by PLIP LFA.52: 2 residues within 4Å: Chain D: L.212, T.216 Ligand excluded by PLIP LFA.54: 2 residues within 4Å: Chain D: L.182 Ligands: LFA.55 Ligand excluded by PLIP LFA.55: 2 residues within 4Å: Chain D: W.208 Ligands: LFA.54 Ligand excluded by PLIP LFA.56: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LFA.58: 4 residues within 4Å: Chain E: L.44, L.48 Ligands: LFA.11, LFA.15 Ligand excluded by PLIP LFA.59: 8 residues within 4Å: Chain A: L.114, I.115, M.119, F.122 Chain E: Y.45, V.256, V.260, N.264 Ligand excluded by PLIP LFA.60: 2 residues within 4Å: Chain E: N.206 Ligands: LFA.61 Ligand excluded by PLIP LFA.61: 4 residues within 4Å: Chain E: L.210, S.253 Ligands: LFA.60, LFA.62 Ligand excluded by PLIP LFA.62: 2 residues within 4Å: Chain E: L.217 Ligands: LFA.61 Ligand excluded by PLIP LFA.63: 1 residues within 4Å: Ligands: LFA.3 Ligand excluded by PLIP LFA.64: 7 residues within 4Å: Chain D: V.260, N.264 Chain E: L.114, R.139, W.143 Ligands: LFA.45, LFA.65 Ligand excluded by PLIP LFA.65: 2 residues within 4Å: Ligands: LFA.48, LFA.64 Ligand excluded by PLIP LFA.66: 3 residues within 4Å: Chain E: N.163, A.166, W.170 Ligand excluded by PLIP LFA.67: 8 residues within 4Å: Chain D: Y.36, Y.76 Chain E: Y.76, A.77, Q.80, N.81, Y.108 Ligands: LFA.40 Ligand excluded by PLIP LFA.68: 2 residues within 4Å: Chain E: A.176, F.177 Ligand excluded by PLIP

5 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)

MPG.13: 4 residues within 4Å: Chain A: I.155, Y.159, N.163, W.170 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.155, A:I.155 Hydrogen bonds: A:N.163 MPG.25: 6 residues within 4Å: Chain B: I.155, Y.159, N.163, A.166, W.170 Ligands: LFA.19 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.155, B:I.155, B:W.170 Hydrogen bonds: B:N.163 MPG.38: 5 residues within 4Å: Chain C: I.155, Y.159, N.163, A.166, W.170 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.155 Hydrogen bonds: C:N.163 MPG.53: 4 residues within 4Å: Chain D: I.155, Y.159, N.163, W.170 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.155 Hydrogen bonds: D:N.163 MPG.69: 4 residues within 4Å: Chain E: Y.159, N.163, A.166, W.170 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gushchin, I. et al., Crystal structure of a light-driven sodium pump. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-04-01

Peptides

Sodium pumping rhodopsin: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Sodium pumping rhodopsin

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