SMTL ID : 4xtn.2 (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: 4 residues within 4Å: Chain A: Y.25, T.83, F.86 Chain B: D.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.86 NA.16: 4 residues within 4Å: Chain B: Y.25, T.83, F.86 Chain C: D.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.25 NA.31: 4 residues within 4Å: Chain C: Y.25, T.83, F.86 Chain D: D.102 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.25, C:F.86 NA.44: 4 residues within 4Å: Chain D: Y.25, T.83, F.86 Chain E: D.102 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:Y.25, E:D.102 NA.58: 4 residues within 4Å: Chain A: D.102 Chain E: Y.25, T.83, F.86 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:F.86

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

LFA.2: 5 residues within 4Å: Chain A: Y.76 Chain B: L.73, Y.76 Ligands: LFA.59, LFA.64 Ligand excluded by PLIP LFA.3: 5 residues within 4Å: Chain A: P.118, R.139 Chain E: V.260, N.264 Ligands: LFA.4 Ligand excluded by PLIP LFA.4: 4 residues within 4Å: Chain A: R.139 Chain E: N.206 Ligands: LFA.3, LFA.61 Ligand excluded by PLIP LFA.5: 3 residues within 4Å: Chain A: F.144, A.147 Ligands: LFA.63 Ligand excluded by PLIP LFA.6: 6 residues within 4Å: Chain A: N.163, T.165, A.166, V.169, W.170, I.173 Ligand excluded by PLIP LFA.7: 3 residues within 4Å: Chain A: V.169, I.173 Ligands: LFA.8 Ligand excluded by PLIP LFA.8: 4 residues within 4Å: Chain A: A.176, F.177, H.180 Ligands: LFA.7 Ligand excluded by PLIP LFA.9: 5 residues within 4Å: Chain A: A.172, S.175, A.176, F.179, W.183 Ligand excluded by PLIP LFA.10: 7 residues within 4Å: Chain A: Y.45, V.256, V.260, N.264 Chain B: V.66, L.114, F.122 Ligand excluded by PLIP LFA.11: 5 residues within 4Å: Chain A: N.206, I.257 Chain B: R.139 Ligands: LFA.12, LFA.19 Ligand excluded by PLIP LFA.12: 5 residues within 4Å: Chain A: N.206, L.210, I.213, S.253 Ligands: LFA.11 Ligand excluded by PLIP LFA.13: 1 residues within 4Å: Chain A: I.249 Ligand excluded by PLIP LFA.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LFA.17: 7 residues within 4Å: Chain A: L.44, I.47, L.48 Chain B: I.47, K.51 Ligands: LFA.18, LFA.22 Ligand excluded by PLIP LFA.18: 6 residues within 4Å: Chain B: Y.76 Chain C: L.73, Y.76 Ligands: LFA.17, LFA.22, LFA.45 Ligand excluded by PLIP LFA.19: 6 residues within 4Å: Chain A: V.260, N.264 Chain B: P.118, R.139, W.143 Ligands: LFA.11 Ligand excluded by PLIP LFA.20: 3 residues within 4Å: Chain B: N.140, F.144, A.147 Ligand excluded by PLIP LFA.21: 5 residues within 4Å: Chain B: N.163, A.166, V.169, W.170, I.173 Ligand excluded by PLIP LFA.22: 6 residues within 4Å: Chain B: I.47, L.48 Chain C: I.47 Ligands: LFA.17, LFA.18, LFA.45 Ligand excluded by PLIP LFA.23: 7 residues within 4Å: Chain B: Y.45, V.256, V.260, N.264 Chain C: L.114, F.122 Ligands: LFA.32 Ligand excluded by PLIP LFA.24: 4 residues within 4Å: Chain B: N.206, L.210, I.249, S.253 Ligand excluded by PLIP LFA.25: 2 residues within 4Å: Chain B: V.246, I.249 Ligand excluded by PLIP LFA.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LFA.28: 2 residues within 4Å: Chain B: A.176, F.177 Ligand excluded by PLIP LFA.29: 2 residues within 4Å: Chain B: L.227, G.229 Ligand excluded by PLIP LFA.30: 7 residues within 4Å: Chain B: L.168, G.171, A.172, S.175, Y.222, L.223, K.255 Ligand excluded by PLIP LFA.32: 4 residues within 4Å: Chain B: N.264 Chain C: P.118 Ligands: LFA.23, LFA.33 Ligand excluded by PLIP LFA.33: 3 residues within 4Å: Chain C: N.140, F.144 Ligands: LFA.32 Ligand excluded by PLIP LFA.34: 5 residues within 4Å: Chain C: N.163, T.165, A.166, V.169, W.170 Ligand excluded by PLIP LFA.35: 8 residues within 4Å: Chain C: L.44, I.47, L.48 Chain D: L.40, L.43, I.47 Ligands: LFA.46, LFA.51 Ligand excluded by PLIP LFA.36: 9 residues within 4Å: Chain C: Y.45, V.256, V.260, N.264 Chain D: V.66, L.114, F.122, F.126 Ligands: LFA.47 Ligand excluded by PLIP LFA.37: 4 residues within 4Å: Chain C: N.206, L.210, I.213, S.253 Ligand excluded by PLIP LFA.38: 1 residues within 4Å: Ligands: LFA.48 Ligand excluded by PLIP LFA.39: 4 residues within 4Å: Chain C: I.23, M.241 Chain D: I.155 Ligands: MPG.57 Ligand excluded by PLIP LFA.40: 1 residues within 4Å: Chain C: D.238 Ligand excluded by PLIP LFA.41: 5 residues within 4Å: Chain C: L.168, G.171, S.175, P.219, K.255 Ligand excluded by PLIP LFA.42: 2 residues within 4Å: Chain C: A.176, F.177 Ligand excluded by PLIP LFA.45: 5 residues within 4Å: Chain C: F.72 Chain D: Y.76 Ligands: LFA.18, LFA.22, LFA.46 Ligand excluded by PLIP LFA.46: 6 residues within 4Å: Chain E: L.73, Y.76 Ligands: LFA.35, LFA.45, LFA.51, LFA.64 Ligand excluded by PLIP LFA.47: 8 residues within 4Å: Chain C: V.260, N.264 Chain D: P.118, F.122, F.135, R.139, W.143 Ligands: LFA.36 Ligand excluded by PLIP LFA.48: 3 residues within 4Å: Chain D: F.144, A.147 Ligands: LFA.38 Ligand excluded by PLIP LFA.49: 6 residues within 4Å: Chain D: N.163, A.166, V.169, W.170, I.173 Ligands: LFA.50 Ligand excluded by PLIP LFA.50: 2 residues within 4Å: Ligands: LFA.49, MPG.57 Ligand excluded by PLIP LFA.51: 7 residues within 4Å: Chain D: I.47, L.48 Chain E: L.40 Ligands: LFA.35, LFA.46, LFA.59, LFA.64 Ligand excluded by PLIP LFA.52: 7 residues within 4Å: Chain D: Y.45, V.252, V.256, V.260, N.264 Chain E: L.114, F.122 Ligand excluded by PLIP LFA.53: 6 residues within 4Å: Chain D: I.209, L.210, I.213, I.249, S.253 Ligands: LFA.54 Ligand excluded by PLIP LFA.54: 2 residues within 4Å: Ligands: LFA.53, LFA.66 Ligand excluded by PLIP LFA.55: 5 residues within 4Å: Chain D: L.168, S.175, P.219, L.223, K.255 Ligand excluded by PLIP LFA.56: 1 residues within 4Å: Chain D: Y.226 Ligand excluded by PLIP LFA.59: 8 residues within 4Å: Chain A: L.43, I.47 Chain E: L.40, L.44, I.47, L.48 Ligands: LFA.2, LFA.51 Ligand excluded by PLIP LFA.60: 12 residues within 4Å: Chain A: L.63, V.66, I.115, M.119, F.122 Chain E: V.38, Y.45, V.252, V.256, V.260, N.264, L.275 Ligand excluded by PLIP LFA.61: 5 residues within 4Å: Chain E: N.206, L.210, I.213, S.253 Ligands: LFA.4 Ligand excluded by PLIP LFA.62: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LFA.63: 1 residues within 4Å: Ligands: LFA.5 Ligand excluded by PLIP LFA.64: 5 residues within 4Å: Chain A: Y.76 Chain E: Y.76 Ligands: LFA.2, LFA.46, LFA.51 Ligand excluded by PLIP LFA.65: 3 residues within 4Å: Chain D: V.260 Chain E: R.139, W.143 Ligand excluded by PLIP LFA.66: 3 residues within 4Å: Chain E: R.139, N.140 Ligands: LFA.54 Ligand excluded by PLIP LFA.67: 4 residues within 4Å: Chain E: N.163, A.166, V.169, W.170 Ligand excluded by PLIP LFA.68: 3 residues within 4Å: Chain E: G.171, S.175, L.223 Ligand excluded by PLIP

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

MPG.15: 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:W.170 Hydrogen bonds: A:N.163 MPG.27: 4 residues within 4Å: Chain B: I.155, Y.159, N.163, W.170 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.155 Hydrogen bonds: B:N.163 MPG.43: 4 residues within 4Å: Chain C: I.155, Y.159, N.163, W.170 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.155 Hydrogen bonds: C:N.163 MPG.57: 7 residues within 4Å: Chain D: I.155, Y.159, N.163, A.166, W.170 Ligands: LFA.39, LFA.50 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: I.155, Y.159, N.163, W.170 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.155 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
F

B
G

C
H

D
I

E
J

Membrane

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

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