SMTL ID : 4xto.1

Crystal structure of the light-driven sodium pump KR2 in the pentameric red form, pH 5.6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 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 B Hydrogen bonds: B:D.102 NA.4: 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:T.83 NA.8: 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.11: 4 residues within 4Å: Chain D: Y.25, T.83, F.86 Chain E: D.102 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.25, D:Y.25 NA.14: 4 residues within 4Å: Chain A: D.102 Chain E: Y.25, T.83, F.86 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Y.25, E:T.83

10 x LFA: EICOSANE(Non-covalent)

LFA.2: 5 residues within 4Å: Chain A: L.63, F.122 Chain E: Y.45, V.256, V.260 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:Y.45, E:Y.45, E:V.256, E:V.260, A:L.63, A:F.122 LFA.3: 4 residues within 4Å: Chain A: Y.45, V.256 Chain B: L.63, V.66 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.45, A:Y.45, A:V.256, B:L.63, B:V.66 LFA.5: 2 residues within 4Å: Chain B: Y.45 Chain C: F.122 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.122, B:Y.45, B:Y.45 LFA.6: 7 residues within 4Å: Chain A: L.44, I.47, L.48 Chain B: L.40, I.47 Ligands: LFA.7, LFA.15 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.47, A:L.48, B:L.40, B:I.47 LFA.7: 4 residues within 4Å: Chain B: L.44, I.47, L.48 Ligands: LFA.6 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.47 LFA.9: 4 residues within 4Å: Chain C: Y.45, V.256, V.260 Chain D: F.122 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.45, C:Y.45, C:V.256, C:V.260, C:V.260, D:F.122 LFA.10: 6 residues within 4Å: Chain C: L.40, L.44, I.47, L.48 Chain D: I.47 Ligands: LFA.13 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.40, C:L.44, C:I.47, C:L.48, D:I.47 LFA.12: 3 residues within 4Å: Chain D: Y.45 Chain E: L.63, F.122 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:Y.45, E:L.63, E:F.122 LFA.13: 5 residues within 4Å: Chain D: L.44, I.47 Chain E: I.47 Ligands: LFA.10, LFA.15 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:I.47, D:I.47 LFA.15: 4 residues within 4Å: Chain E: L.44, I.47 Ligands: LFA.6, LFA.13 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.47

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.
Show / Hide

Sodium pumping rhodopsin

Related Entries With Identical Sequence