SMTL ID : 5jrf.1

Crystal structure of the light-driven sodium pump KR2 bound with iodide ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

8 x LFA: EICOSANE(Non-covalent)

LFA.1: 2 residues within 4Å: Chain A: Y.45, N.264 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.45, A:Y.45, A:Y.45 LFA.2: 3 residues within 4Å: Chain A: F.72, Y.76 Ligands: IOD.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.72, A:Y.76 LFA.3: 5 residues within 4Å: Chain A: N.105, G.107, Y.108, Y.110, Y.154 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.108, A:Y.110, A:Y.154, A:Y.154 LFA.4: 3 residues within 4Å: Chain A: L.48, T.49, N.52 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.48, A:T.49 LFA.5: 1 residues within 4Å: Chain A: I.257 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.257 LFA.6: 5 residues within 4Å: Chain A: N.163, T.165, V.169, W.170, I.173 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.165, A:V.169, A:W.170, A:I.173 LFA.7: 1 residues within 4Å: Chain A: K.186 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.186 LFA.8: 3 residues within 4Å: Chain A: F.179, H.180, W.183 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.179, A:W.183, A:W.183, A:W.183

20 x IOD: IODIDE ION(Non-functional Binders)

IOD.9: 3 residues within 4Å: Chain A: Y.110, R.243, Y.247 Ligand excluded by PLIP IOD.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: F.122, R.139 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: F.27, H.30 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Ligands: LFA.2 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: Y.159, S.162, N.163 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: F.135, S.136 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: S.197, L.269 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain A: Q.141 Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain A: W.208 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain A: K.193 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: I.203, N.206 Ligand excluded by PLIP IOD.21: 1 residues within 4Å: Chain A: A.199 Ligand excluded by PLIP IOD.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.23: 4 residues within 4Å: Chain A: E.18, R.94, S.236, E.237 Ligand excluded by PLIP IOD.24: 3 residues within 4Å: Chain A: D.54, K.55, K.56 Ligand excluded by PLIP IOD.25: 1 residues within 4Å: Chain A: F.126 Ligand excluded by PLIP IOD.26: 2 residues within 4Å: Chain A: D.54, K.55 Ligand excluded by PLIP IOD.27: 1 residues within 4Å: Chain A: L.130 Ligand excluded by PLIP IOD.28: 1 residues within 4Å: Chain A: N.140 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Melnikov, I. et al., Fast iodide-SAD phasing for high-throughput membrane protein structure determination. Sci Adv (2017)

Release Date

2017-05-31

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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