SMTL ID : 6rfa.1

Crystal structure of the H30K mutant of the light-driven sodium pump KR2 in the monomeric form, pH 8.0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.83

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

LFA.2: 4 residues within 4Å: Chain A: F.72, L.73, Y.76 Ligands: LFA.33 Ligand excluded by PLIP LFA.3: 3 residues within 4Å: Chain A: N.163, V.169, W.170 Ligand excluded by PLIP LFA.4: 7 residues within 4Å: Chain A: T.248, I.249, S.253, I.257 Ligands: LFA.25, LFA.30, LFA.31 Ligand excluded by PLIP LFA.5: 2 residues within 4Å: Ligands: LFA.11, LFA.36 Ligand excluded by PLIP LFA.6: 4 residues within 4Å: Chain A: G.107, Y.108, L.111, Y.154 Ligand excluded by PLIP LFA.7: 5 residues within 4Å: Chain A: A.41, Y.45, L.48, N.52 Ligands: LFA.16 Ligand excluded by PLIP LFA.8: 5 residues within 4Å: Chain A: L.168, Y.226, G.229, V.230 Ligands: LFA.12 Ligand excluded by PLIP LFA.9: 2 residues within 4Å: Chain A: R.139, N.140 Ligand excluded by PLIP LFA.10: 5 residues within 4Å: Chain A: N.206, L.210, I.213, S.253 Ligands: LFA.25 Ligand excluded by PLIP LFA.11: 6 residues within 4Å: Chain A: V.260, L.261, N.264 Ligands: LFA.5, LFA.25, LFA.36 Ligand excluded by PLIP LFA.12: 7 residues within 4Å: Chain A: L.168, G.171, A.172, S.175, L.223 Ligands: LFA.8, LFA.34 Ligand excluded by PLIP LFA.13: 1 residues within 4Å: Ligands: LFA.29 Ligand excluded by PLIP LFA.14: 3 residues within 4Å: Chain A: T.33 Ligands: LFA.15, LFA.22 Ligand excluded by PLIP LFA.15: 3 residues within 4Å: Chain A: A.41, L.44 Ligands: LFA.14 Ligand excluded by PLIP LFA.16: 2 residues within 4Å: Ligands: LFA.7, LFA.36 Ligand excluded by PLIP LFA.17: 3 residues within 4Å: Chain A: I.173 Ligands: LFA.19, LFA.28 Ligand excluded by PLIP LFA.18: 3 residues within 4Å: Chain A: M.59, F.122 Ligands: LFA.24 Ligand excluded by PLIP LFA.19: 3 residues within 4Å: Chain A: F.144, H.180 Ligands: LFA.17 Ligand excluded by PLIP LFA.20: 3 residues within 4Å: Chain A: M.59 Ligands: LFA.27, LFA.33 Ligand excluded by PLIP LFA.21: 2 residues within 4Å: Chain A: K.30 Ligands: LFA.36 Ligand excluded by PLIP LFA.22: 4 residues within 4Å: Chain A: Y.36, Y.76, Q.80 Ligands: LFA.14 Ligand excluded by PLIP LFA.23: 1 residues within 4Å: Chain A: M.241 Ligand excluded by PLIP LFA.24: 4 residues within 4Å: Chain A: F.122, F.135, R.139 Ligands: LFA.18 Ligand excluded by PLIP LFA.25: 5 residues within 4Å: Chain A: N.206, I.257 Ligands: LFA.4, LFA.10, LFA.11 Ligand excluded by PLIP LFA.26: 3 residues within 4Å: Chain A: L.227, T.228, G.229 Ligand excluded by PLIP LFA.27: 1 residues within 4Å: Ligands: LFA.20 Ligand excluded by PLIP LFA.28: 1 residues within 4Å: Ligands: LFA.17 Ligand excluded by PLIP LFA.29: 3 residues within 4Å: Chain A: G.220, M.224 Ligands: LFA.13 Ligand excluded by PLIP LFA.30: 3 residues within 4Å: Chain A: I.249 Ligands: LFA.4, LFA.31 Ligand excluded by PLIP LFA.31: 3 residues within 4Å: Chain A: I.31 Ligands: LFA.4, LFA.30 Ligand excluded by PLIP LFA.32: 4 residues within 4Å: Chain A: I.115, P.118, M.119, W.143 Ligand excluded by PLIP LFA.33: 4 residues within 4Å: Chain A: V.66, A.77 Ligands: LFA.2, LFA.20 Ligand excluded by PLIP LFA.34: 3 residues within 4Å: Chain A: T.165 Ligands: LFA.12, GOL.35 Ligand excluded by PLIP LFA.36: 9 residues within 4Å: Chain A: L.34, A.41, G.42, Y.45, N.264 Ligands: LFA.5, LFA.11, LFA.16, LFA.21 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.35: 3 residues within 4Å: Chain A: N.163, T.165 Ligands: LFA.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.165, A:T.165, A:T.165

1 x RET: RETINAL(Covalent)

RET.37: 13 residues within 4Å: Chain A: W.113, L.120, M.149, G.171, S.174, S.175, F.178, W.215, Y.218, P.219, Y.222, S.254, K.255 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.113, A:F.178, A:W.215, A:W.215, A:Y.218, A:Y.218, A:Y.218, A:Y.218, A:P.219, A:Y.222, A:K.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovalev, K. et al., Structure and mechanisms of sodium-pumping KR2 rhodopsin. Sci Adv (2019)

Release Date

2019-04-24

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