SMTL ID : 7y6i.1

Cryo-EM structure of human sodium-chloride cotransporter

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: V.408, T.409, G.413, A.414, C.415, N.425, T.427, E.428 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 9 residues within 4Å: Chain B: V.408, T.409, G.413, A.414, C.415, N.425, T.427, E.428, Q.431 No protein-ligand interaction detected (PLIP)

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

CL.3: 8 residues within 4Å: Chain A: I.149, G.151, V.152, I.153, H.233, P.348, S.349 Ligands: NA.4 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain A: F.222, G.352, I.353, L.354, F.535, Y.539 Ligand excluded by PLIP CL.22: 8 residues within 4Å: Chain B: I.149, G.151, V.152, I.153, H.233, P.348, S.349 Ligands: NA.23 Ligand excluded by PLIP CL.24: 6 residues within 4Å: Chain B: F.222, G.352, I.353, L.354, F.535, Y.539 Ligand excluded by PLIP

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

NA.4: 6 residues within 4Å: Chain A: N.148, I.149, H.233, P.348, T.351 Ligands: CL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.233 NA.6: 5 residues within 4Å: Chain A: L.147, W.150, A.463, S.466, S.467 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.467, A:S.467 NA.23: 6 residues within 4Å: Chain B: N.148, I.149, H.233, P.348, T.351 Ligands: CL.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.233 NA.25: 5 residues within 4Å: Chain B: L.147, W.150, A.463, S.466, S.467 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.150, B:S.467

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 8 residues within 4Å: Chain A: T.179, N.565, W.567, A.568, F.571 Ligands: Y01.8, Y01.9, LPE.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.179, A:N.565, A:W.567, A:A.568, A:F.571, A:F.571, A:F.571, A:F.571 Y01.8: 12 residues within 4Å: Chain A: L.169, I.172, L.176, P.330, W.332, F.339, F.340, F.571, I.575 Ligands: Y01.7, LPE.10, LPE.12 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.169, A:L.176, A:P.330, A:F.339, A:F.339, A:F.339, A:F.339, A:F.340, A:F.340, A:F.571, A:I.575 Y01.9: 8 residues within 4Å: Chain A: W.567, L.570, F.571, I.574, I.575 Ligands: Y01.7, LPE.12, POV.14 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.567, A:W.567, A:W.567, A:L.570, A:F.571, A:F.571, A:I.574, A:I.574, A:I.575 Y01.26: 7 residues within 4Å: Chain B: T.179, I.183, N.565, W.567, F.571 Ligands: Y01.28, LPE.29 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.179, B:I.183, B:F.571, B:F.571 Y01.27: 11 residues within 4Å: Chain B: L.169, I.172, L.176, P.330, W.332, F.339, F.340, F.571, I.575 Ligands: LPE.29, LPE.31 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.169, B:I.172, B:L.176, B:L.176, B:P.330, B:F.339, B:F.339, B:F.339, B:F.339, B:F.339, B:F.339, B:F.340, B:F.340, B:F.571, B:I.575 Y01.28: 7 residues within 4Å: Chain B: W.567, F.571, I.574, I.575 Ligands: Y01.26, LPE.31, POV.33 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.567, B:W.567, B:W.567, B:W.567, B:F.571, B:F.571, B:F.571, B:I.574, B:I.574, B:I.575

8 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

LPE.10: 8 residues within 4Å: Chain A: T.179, S.182, L.186, Q.562, Y.563, N.565 Ligands: Y01.7, Y01.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.186 Hydrogen bonds: A:Q.562 LPE.11: 16 residues within 4Å: Chain A: V.178, T.193, A.367, I.368, P.371, K.372, L.375, M.376, I.378, F.379, T.382, I.383, S.560, F.561, Q.562, Y.563 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.178, A:L.375, A:L.375, A:L.375, A:I.378, A:F.379, A:F.379, A:T.382, A:I.383 LPE.12: 10 residues within 4Å: Chain A: D.336, T.338, F.340, I.574, L.582, L.583 Chain B: W.585 Ligands: Y01.8, Y01.9, POV.21 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.574, A:L.582 Hydrogen bonds: A:T.338, A:T.338, A:G.341 LPE.13: 11 residues within 4Å: Chain A: W.137, V.138, M.142, M.146, F.289, F.296, L.300, W.380, S.384, I.388 Ligands: POV.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.289, A:F.296, A:L.300, A:W.380, A:I.388 LPE.29: 8 residues within 4Å: Chain B: L.175, T.179, S.182, Q.562, Y.563, N.565 Ligands: Y01.26, Y01.27 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.175 Hydrogen bonds: B:Q.562 LPE.30: 10 residues within 4Å: Chain B: V.178, K.372, L.375, M.376, F.379, T.382, I.383, L.386, F.561, Q.562 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.178, B:L.375, B:F.379, B:T.382, B:I.383, B:L.386 LPE.31: 7 residues within 4Å: Chain B: T.338, F.340, L.582 Ligands: POV.17, Y01.27, Y01.28, POV.33 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.340, B:L.582 LPE.32: 8 residues within 4Å: Chain B: V.138, M.142, M.146, L.300, W.380, S.384, A.387, I.388 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.300, B:L.300, B:W.380, B:W.380, B:A.387, B:I.388

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

POV.14: 21 residues within 4Å: Chain A: C.537, A.540, L.541, F.544, I.551, K.566, W.567, L.570, A.573, I.574, V.577, I.592 Chain B: G.593, L.596, F.597, L.600, Y.601, Y.604 Ligands: Y01.9, POV.18, POV.21 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.540, A:L.541, A:F.544, A:F.544, A:F.544, A:F.544, A:W.567, A:L.570, A:A.573, A:I.574, A:I.592, B:L.596, B:F.597, B:F.597 Salt bridges: A:K.566 POV.15: 11 residues within 4Å: Chain A: W.171, Y.319, R.320, A.321, F.324, I.383, A.387, A.390, T.391, S.394 Ligands: LPE.13 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.171, A:Y.319, A:Y.319, A:Y.319, A:F.324, A:A.387, A:A.390, A:A.390 Hydrogen bonds: A:A.321 POV.16: 13 residues within 4Å: Chain A: L.220, I.221, F.224, R.260, A.517, F.518, I.520, I.521, T.526, F.534, W.586, I.590, V.594 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.220, A:I.221, A:F.224, A:F.224, A:F.224, A:F.224, A:F.224, A:F.518, A:F.518, A:I.520, A:I.521, A:F.534, A:F.534, A:W.586, A:W.586, A:I.590, A:V.594 Hydrogen bonds: A:R.260 POV.17: 11 residues within 4Å: Chain A: T.584, W.585, W.586, L.589, I.590, L.596, F.597 Chain B: V.577 Ligands: POV.18, LPE.31, POV.33 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.585, A:W.586, A:W.586, A:W.586, A:L.589, A:L.589, A:I.590, A:I.590, A:I.590, A:L.596, A:F.597, B:V.577 POV.18: 21 residues within 4Å: Chain A: E.213, F.544, H.548, T.552, I.592, V.595, L.596, L.599, L.600 Chain B: E.213, F.544, H.548, I.592, L.596, L.599, L.600, I.603, Y.604 Ligands: POV.14, POV.17, POV.21 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:F.544, B:I.592, B:L.596, B:L.599, B:L.599, B:I.603, A:F.544, A:I.592, A:V.595, A:L.596, A:L.596, A:L.596, A:L.599, A:L.600 Salt bridges: A:H.548, A:H.548 POV.20: 10 residues within 4Å: Chain B: L.220, I.221, F.224, A.517, F.518, I.521, T.526, F.534, W.586, V.594 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.220, B:I.221, B:F.224, B:F.224, B:F.224, B:F.224, B:F.518, B:F.518, B:I.521, B:F.534, B:V.594 POV.21: 10 residues within 4Å: Chain A: V.577 Chain B: W.585, W.586, L.589, I.590, V.594, L.596 Ligands: LPE.12, POV.14, POV.18 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.586, B:W.586, B:W.586, B:W.586, B:L.589, B:I.590, B:I.590, B:V.594, B:L.596, A:V.577 POV.33: 22 residues within 4Å: Chain A: G.593, L.596, F.597, L.600, Y.601, Y.604 Chain B: C.537, A.540, L.541, F.544, F.547, I.551, K.566, W.567, L.570, I.574, V.577, I.592, V.595 Ligands: POV.17, Y01.28, LPE.31 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:L.596, A:F.597, A:L.600, A:Y.604, B:A.540, B:L.541, B:F.544, B:F.544, B:F.544, B:F.547, B:W.567, B:L.570, B:I.574, B:I.592, B:V.595 POV.34: 11 residues within 4Å: Chain B: W.171, L.300, Y.319, R.320, A.321, D.322, F.324, I.383, L.386, A.390, S.394 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.171, B:W.171, B:L.300, B:Y.319, B:Y.319, B:F.324, B:I.383, B:L.386, B:A.390 Hydrogen bonds: B:A.321

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.19: 3 residues within 4Å: Chain A: V.403, L.404, N.405 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.403 Hydrogen bonds: A:L.404, A:N.405 NAG.35: 1 residues within 4Å: Chain B: N.405 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.405

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nan, J. et al., Cryo-EM structure of the human sodium-chloride cotransporter NCC. Sci Adv (2022)

Release Date

2022-11-23

Peptides

Solute carrier family 12 member 3: 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 3

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