SMTL ID : 4xtl.1

Crystal structure of the light-driven sodium pump KR2 in the monomeric blue form, pH 4.3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: Y.25, T.83, F.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.25 Water bridges: A:Y.25

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

LFA.2: 8 residues within 4Å: Chain A: V.38, A.41, G.42, Y.45, V.260, N.264 Ligands: LFA.6, LFA.17 Ligand excluded by PLIP LFA.3: 2 residues within 4Å: Chain A: L.73, Y.76 Ligand excluded by PLIP LFA.4: 6 residues within 4Å: Chain A: N.163, T.165, A.166, V.169, W.170, I.173 Ligand excluded by PLIP LFA.5: 6 residues within 4Å: Chain A: I.249, S.253, I.257 Ligands: LFA.12, LFA.26, LFA.32 Ligand excluded by PLIP LFA.6: 2 residues within 4Å: Ligands: LFA.2, LFA.12 Ligand excluded by PLIP LFA.7: 7 residues within 4Å: Chain A: N.105, G.107, Y.108, Y.110, L.111, I.151, Y.154 Ligand excluded by PLIP LFA.8: 4 residues within 4Å: Chain A: A.41, Y.45, T.49 Ligands: LFA.17 Ligand excluded by PLIP LFA.9: 5 residues within 4Å: Chain A: L.164, L.168, Y.226, V.230 Ligands: LFA.13 Ligand excluded by PLIP LFA.10: 3 residues within 4Å: Chain A: R.139, N.140, F.144 Ligand excluded by PLIP LFA.11: 6 residues within 4Å: Chain A: N.206, I.209, L.210, I.213, S.253 Ligands: LFA.26 Ligand excluded by PLIP LFA.12: 5 residues within 4Å: Chain A: I.257, V.260, N.264 Ligands: LFA.5, LFA.6 Ligand excluded by PLIP LFA.13: 6 residues within 4Å: Chain A: L.168, G.171, A.172, S.175, L.223 Ligands: LFA.9 Ligand excluded by PLIP LFA.14: 4 residues within 4Å: Chain A: S.175, P.219, G.220 Ligands: LFA.30 Ligand excluded by PLIP LFA.15: 4 residues within 4Å: Chain A: T.33, Y.36 Ligands: LFA.16, LFA.23 Ligand excluded by PLIP LFA.16: 4 residues within 4Å: Chain A: A.37, A.41 Ligands: LFA.15, LFA.17 Ligand excluded by PLIP LFA.17: 3 residues within 4Å: Ligands: LFA.2, LFA.8, LFA.16 Ligand excluded by PLIP LFA.18: 8 residues within 4Å: Chain A: M.148, I.151, T.152, I.155, W.170, I.173, A.176 Ligands: LFA.20 Ligand excluded by PLIP LFA.19: 6 residues within 4Å: Chain A: M.59, F.122, F.126 Ligands: LFA.21, LFA.25, LFA.33 Ligand excluded by PLIP LFA.20: 7 residues within 4Å: Chain A: Q.141, F.144, S.145, A.176, F.177, H.180 Ligands: LFA.18 Ligand excluded by PLIP LFA.21: 4 residues within 4Å: Chain A: M.59 Ligands: LFA.19, LFA.28, LFA.33 Ligand excluded by PLIP LFA.22: 3 residues within 4Å: Chain A: H.30, T.33, L.34 Ligand excluded by PLIP LFA.23: 3 residues within 4Å: Chain A: Y.36, Y.76 Ligands: LFA.15 Ligand excluded by PLIP LFA.24: 2 residues within 4Å: Chain A: F.233, D.238 Ligand excluded by PLIP LFA.25: 5 residues within 4Å: Chain A: F.122, F.126, F.135, R.139 Ligands: LFA.19 Ligand excluded by PLIP LFA.26: 4 residues within 4Å: Chain A: N.206, L.261 Ligands: LFA.5, LFA.11 Ligand excluded by PLIP LFA.27: 4 residues within 4Å: Chain A: Y.226, L.227, T.228, G.229 Ligand excluded by PLIP LFA.28: 2 residues within 4Å: Chain A: M.59 Ligands: LFA.21 Ligand excluded by PLIP LFA.29: 1 residues within 4Å: Chain A: W.170 Ligand excluded by PLIP LFA.30: 5 residues within 4Å: Chain A: T.216, L.217, G.220, M.224 Ligands: LFA.14 Ligand excluded by PLIP LFA.31: 1 residues within 4Å: Chain A: I.249 Ligand excluded by PLIP LFA.32: 3 residues within 4Å: Chain A: I.31, L.245 Ligands: LFA.5 Ligand excluded by PLIP LFA.33: 6 residues within 4Å: Chain A: L.114, P.118, M.119, W.143 Ligands: LFA.19, LFA.21 Ligand excluded by PLIP LFA.34: 4 residues within 4Å: Chain A: V.66, S.70, L.73, L.74 Ligand excluded by PLIP LFA.35: 3 residues within 4Å: Chain A: L.164, L.168 Ligands: GOL.36 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.36: 4 residues within 4Å: Chain A: N.163, L.164, T.165 Ligands: LFA.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.165, A:T.165, A:T.165 GOL.37: 3 residues within 4Å: Chain A: F.179, K.186, W.208 No protein-ligand interaction detected (PLIP)

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

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

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