SMTL ID : 7zgo.1

Cryo-EM structure of human NKCC1 (TM domain)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

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

NA.1: 6 residues within 4Å: Chain A: L.301, W.304, G.305, A.614, S.617, S.618 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.304, A:S.618 NA.12: 6 residues within 4Å: Chain B: L.301, W.304, G.305, A.614, S.617, S.618 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.301, B:S.618

2 x K: POTASSIUM ION(Non-covalent)

K.2: 7 residues within 4Å: Chain A: N.302, I.303, Y.387, P.500, A.501, T.503 Ligands: CL.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.302, A:I.303, A:Y.387, A:P.500, A:T.503 K.13: 7 residues within 4Å: Chain B: N.302, I.303, Y.387, P.500, A.501, T.503 Ligands: CL.15 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:N.302, B:I.303, B:Y.387, B:P.500, B:T.503

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 8 residues within 4Å: Chain A: I.303, G.305, V.306, M.307, Y.387, P.500, A.501 Ligands: K.2 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain A: F.376, G.504, I.505, L.506, F.686, Y.690 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain B: F.376, G.504, I.505, L.506, F.686, Y.690 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain B: I.303, G.305, V.306, M.307, Y.387, P.500, A.501 Ligands: K.13 Ligand excluded by PLIP

7 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.5: 22 residues within 4Å: Chain A: A.688, A.691, L.692, F.695, F.698, L.702, K.704, W.718, L.721, A.724, C.728, Y.743, V.746 Chain B: L.747, G.748, L.749, I.751, Y.752, Y.755, K.757 Ligands: POV.7, POV.8 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:A.691, A:L.692, A:F.695, A:F.698, A:W.718, A:A.724, A:Y.743, A:V.746, B:L.747, B:L.749, B:I.751, B:Y.752 Salt bridges: B:K.757 POV.6: 14 residues within 4Å: Chain A: F.492, L.726, I.729, V.733, I.734, N.735, W.737 Chain B: W.736, W.737, L.741, V.744 Ligands: POV.7, Y01.9, POV.16 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.492, A:F.492, A:L.726, A:I.729, A:V.733, B:W.736, B:W.737, B:W.737, B:V.744, B:V.744 POV.7: 8 residues within 4Å: Chain A: M.717, W.718, L.722, I.725, I.729 Chain B: L.741 Ligands: POV.5, POV.6 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.718, A:W.718, A:W.718, A:L.722, A:I.725, A:I.729, B:L.741 POV.8: 26 residues within 4Å: Chain A: F.695, H.699, C.728, F.732, L.740, Y.743, V.746, L.747, Y.750, T.754, Y.755 Chain B: F.368, F.695, H.699, C.728, F.732, L.740, Y.743, V.744, V.746, L.747, Y.750, T.754, Y.755 Ligands: POV.5, POV.17 23 PLIP interactions: 13 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.695, A:F.732, A:L.740, A:Y.743, A:Y.743, A:V.746, A:L.747, A:L.747, A:Y.750, A:Y.750, B:F.368, B:F.732, B:L.740, B:Y.743, B:V.744, B:V.746, B:L.747, B:L.747, B:Y.750, B:Y.755 Hydrogen bonds: A:T.754, A:Y.755 Salt bridges: A:H.699 POV.16: 12 residues within 4Å: Chain A: W.736, W.737, L.740 Chain B: T.490, F.492, I.729, V.733, I.734, N.735, W.737 Ligands: POV.6, POV.18 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.736, A:W.737, A:L.740, B:F.492, B:F.492, B:F.492, B:V.733 POV.17: 23 residues within 4Å: Chain A: I.745, L.747, G.748, I.751, Y.752, Y.755, K.756, K.757 Chain B: A.691, L.692, F.695, F.698, L.702, K.704, W.718, L.721, A.724, I.725, C.728, Y.743, V.746 Ligands: POV.8, POV.18 19 PLIP interactions: 11 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:A.691, B:L.692, B:L.692, B:F.695, B:F.698, B:F.698, B:L.721, B:A.724, B:I.725, B:Y.743, B:V.746, A:I.745, A:I.745, A:I.751, A:I.751, A:Y.752, A:Y.752, A:Y.752 Salt bridges: A:K.757 POV.18: 10 residues within 4Å: Chain A: V.744 Chain B: Y.715, N.716, M.717, W.718, L.722, I.725, L.726 Ligands: POV.16, POV.17 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.718, B:W.718, B:W.718, B:W.718, B:I.725, B:I.725, B:L.726, A:V.744 Hydrogen bonds: B:N.716

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.9: 8 residues within 4Å: Chain A: L.326, M.330, V.333, P.483, F.485, F.491, F.492 Ligands: POV.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.326, A:V.333, A:P.483, A:F.485, A:F.491, A:F.491, A:F.492 Hydrogen bonds: A:F.491 Y01.10: 9 residues within 4Å: Chain A: F.458, Y.472, K.473, S.474, G.539, I.540, V.542, S.543, S.546 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.458, A:I.540, A:V.542 Hydrogen bonds: A:S.474 Y01.11: 5 residues within 4Å: Chain A: L.447, I.450, G.451, V.454, I.455 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.450, A:V.454, A:I.455 Y01.19: 7 residues within 4Å: Chain B: L.326, M.329, M.330, P.483, F.485, F.491, F.492 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.326, B:M.329, B:P.483, B:F.491, B:F.491, B:F.492 Y01.20: 9 residues within 4Å: Chain B: V.454, F.458, Y.472, S.474, L.535, G.539, V.542, S.543, S.546 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.454, B:F.458, B:Y.472 Hydrogen bonds: B:S.474 Y01.21: 5 residues within 4Å: Chain B: L.447, I.450, G.451, V.454, I.455 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.450, B:V.454, B:I.455

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neumann, C. et al., Cryo-EM structure of the human NKCC1 transporter reveals mechanisms of ion coupling and specificity. Embo J. (2022)

Release Date

2022-10-05

Peptides

Solute carrier family 12 member 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Solute carrier family 12 member 2