SMTL ID : 6rf0.1

Crystal structure of the light-driven sodium pump KR2 in the pentameric "dry" form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 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 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:Y.25 NA.6: 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.12: 4 residues within 4Å: Chain C: Y.25, T.83, F.86 Chain D: D.102 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.86 NA.17: 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

5 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.2: 4 residues within 4Å: Chain A: Y.159, N.163, A.166, W.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.163 OLC.9: 3 residues within 4Å: Chain B: Y.159, N.163, W.170 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.163 OLC.14: 3 residues within 4Å: Chain C: Y.159, N.163, W.170 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.159 Hydrogen bonds: C:N.163 OLC.19: 5 residues within 4Å: Chain D: I.155, Y.159, N.163, A.166, W.170 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.155 Hydrogen bonds: D:N.163 OLC.23: 4 residues within 4Å: Chain E: Y.159, N.163, A.166, W.170 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.163

10 x LFA: EICOSANE(Non-covalent)

LFA.3: 10 residues within 4Å: Chain A: V.38, Y.45, V.256, V.260, N.264, V.276 Chain B: L.63, V.66, I.115, F.122 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.38, A:Y.45, A:Y.45, A:V.256, A:V.260, B:V.66, B:I.115 LFA.7: 6 residues within 4Å: Chain A: L.40, I.47 Chain B: L.40, I.47 Ligands: LFA.8, LFA.22 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.40, A:I.47, B:L.40, B:I.47, B:I.47 LFA.8: 6 residues within 4Å: Chain B: L.44, I.47 Chain C: L.40, I.47 Ligands: LFA.7, LFA.13 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.47, C:L.40, C:I.47 LFA.10: 8 residues within 4Å: Chain B: V.38, Y.45, V.256, N.264, V.276 Chain C: V.66, I.115, F.122 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:V.66, C:I.115, C:F.122, B:V.38, B:Y.45, B:Y.45, B:V.256, B:V.276 LFA.13: 7 residues within 4Å: Chain C: L.40, L.44, I.47, L.48 Chain D: I.47 Ligands: LFA.8, LFA.18 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.40, C:L.44, C:I.47, C:L.48, D:I.47, D:I.47 LFA.15: 8 residues within 4Å: Chain C: V.38, Y.45, V.256, N.264, V.276 Chain D: I.115, M.119, F.122 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.38, C:Y.45, C:V.256, D:I.115, D:F.122 LFA.18: 7 residues within 4Å: Chain D: L.40, L.44, I.47 Chain E: L.40, I.47 Ligands: LFA.13, LFA.22 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:L.40, E:I.47, E:I.47, D:L.40, D:L.44, D:I.47, D:I.47 LFA.20: 10 residues within 4Å: Chain D: V.38, Y.45, V.256, N.264, V.276 Chain E: M.59, L.63, I.115, M.119, F.122 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.63, E:I.115, E:F.122, D:Y.45, D:Y.45, D:V.256 LFA.22: 6 residues within 4Å: Chain A: I.47 Chain E: L.40, L.44, I.47 Ligands: LFA.7, LFA.18 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:L.40, E:I.47, E:I.47, A:I.47 LFA.24: 10 residues within 4Å: Chain A: L.63, V.66, I.115, F.122 Chain E: Y.45, V.256, I.257, V.260, N.264, V.276 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain E Hydrophobic interactions: A:L.63, A:V.66, A:I.115, A:F.122, E:Y.45, E:Y.45, E:V.256, E:I.257, E:V.260

5 x RET: RETINAL(Covalent)

RET.5: 15 residues within 4Å: Chain A: W.113, V.117, L.120, M.149, G.153, G.171, S.174, F.178, W.215, Y.218, P.219, Y.222, D.251, S.254, K.255 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.113, A:V.117, A:F.178, 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 RET.11: 15 residues within 4Å: Chain B: W.113, V.117, L.120, M.149, G.153, G.171, S.174, F.178, W.215, Y.218, P.219, Y.222, D.251, S.254, K.255 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.113, B:V.117, B:F.178, B:F.178, B:W.215, B:W.215, B:Y.218, B:Y.218, B:Y.218, B:Y.218, B:P.219, B:Y.222, B:K.255 RET.16: 15 residues within 4Å: Chain C: W.113, V.117, L.120, M.149, G.153, G.171, S.174, F.178, W.215, Y.218, P.219, Y.222, D.251, S.254, K.255 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.113, C:V.117, C:F.178, C:F.178, C:W.215, C:W.215, C:Y.218, C:Y.218, C:Y.218, C:Y.218, C:P.219, C:Y.222, C:K.255 RET.21: 15 residues within 4Å: Chain D: W.113, V.117, L.120, M.149, G.153, G.171, S.174, F.178, W.215, Y.218, P.219, Y.222, D.251, S.254, K.255 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:W.113, D:V.117, D:F.178, D:F.178, D:W.215, D:W.215, D:Y.218, D:Y.218, D:Y.218, D:Y.218, D:P.219, D:Y.222, D:K.255 RET.25: 15 residues within 4Å: Chain E: W.113, V.117, L.120, M.149, G.153, G.171, S.174, F.178, W.215, Y.218, P.219, Y.222, D.251, S.254, K.255 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:W.113, E:V.117, E:F.178, E:F.178, E:W.215, E:W.215, E:Y.218, E:Y.218, E:Y.218, E:Y.218, E:P.219, E:Y.222, E: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: 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