SMTL ID : 8x1u.1

Cryo-EM structure of human DRA (SLC26A3) bound with oxalate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x OXL: OXALATE ION(Non-covalent)

OXL.1: 8 residues within 4Å: Chain A: F.141, P.142, I.143, T.406, A.407, L.408, S.409, M.462 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.143, A:L.408, A:S.409 OXL.43: 8 residues within 4Å: Chain B: F.141, P.142, I.143, T.406, A.407, L.408, S.409, M.462 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.143, B:L.408, B:S.409

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

POV.2: 11 residues within 4Å: Chain A: F.204, Q.348, V.351, G.352, F.355, M.359 Ligands: C14.3, D10.24, LPE.25, D12.26, LPE.64 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.204, A:V.351, A:V.351, A:F.355, A:F.355 POV.40: 9 residues within 4Å: Chain A: F.255, F.466, I.469, G.470, F.487, I.488, I.491 Ligands: LPE.39, D12.41 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.255, A:F.466, A:I.469, A:F.487, A:I.488, A:I.491 Hydrogen bonds: A:G.470 POV.83: 13 residues within 4Å: Chain B: F.204, I.209, Q.348, V.351, G.352, F.355, M.359 Ligands: LPE.22, C14.23, C14.44, D10.66, LPE.67, D12.68 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.204, B:I.209, B:V.351, B:F.355, B:F.355, B:F.355, B:F.355 POV.84: 11 residues within 4Å: Chain B: V.230, F.255, F.466, A.467, I.469, G.470, R.474, F.487, I.488 Ligands: LPE.81, D12.82 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.230, B:F.255, B:F.466, B:A.467, B:I.469, B:F.487, B:I.488 Hydrogen bonds: B:G.470

8 x C14: TETRADECANE(Non-covalent)

C14.3: 5 residues within 4Å: Chain A: A.203, F.204, Q.348, F.355 Ligands: POV.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.203, A:F.204, A:F.355 C14.7: 3 residues within 4Å: Chain A: F.122, F.336, F.399 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.122, A:F.336 C14.23: 7 residues within 4Å: Chain A: A.504, F.505, L.508 Ligands: LPE.22, D10.66, LPE.67, POV.83 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.504, A:F.505, A:L.508 C14.35: 1 residues within 4Å: Chain A: P.302 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.302 C14.44: 3 residues within 4Å: Chain B: A.203, Q.348 Ligands: POV.83 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.203, B:Q.348 C14.48: 3 residues within 4Å: Chain B: F.122, F.336, F.399 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.122, B:F.336 C14.65: 7 residues within 4Å: Chain B: L.493, A.501, A.504, F.505 Ligands: D10.24, LPE.25, LPE.64 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.493, B:A.504 C14.77: 1 residues within 4Å: Chain B: P.302 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.302

16 x D12: DODECANE(Non-covalent)(Non-functional Binders)

D12.4: 5 residues within 4Å: Chain A: I.199, T.341, P.342, V.344 Ligands: LPE.5 Ligand excluded by PLIP D12.9: 2 residues within 4Å: Chain A: L.433, L.437 Ligand excluded by PLIP D12.21: 7 residues within 4Å: Chain A: F.255, L.258, Y.259, F.262, S.263 Ligands: D10.20, CLR.42 Ligand excluded by PLIP D12.26: 5 residues within 4Å: Chain A: L.207, R.208, F.211 Chain B: F.516 Ligands: POV.2 Ligand excluded by PLIP D12.32: 4 residues within 4Å: Chain A: L.75, Y.78, L.80 Ligands: D10.33 Ligand excluded by PLIP D12.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP D12.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP D12.41: 4 residues within 4Å: Chain A: I.469, W.473, I.484 Ligands: POV.40 Ligand excluded by PLIP D12.45: 5 residues within 4Å: Chain B: I.199, T.341, P.342, V.344 Ligands: LPE.46 Ligand excluded by PLIP D12.50: 1 residues within 4Å: Chain B: L.433 Ligand excluded by PLIP D12.62: 4 residues within 4Å: Chain B: Y.259, S.263 Ligands: D10.61, CLR.63 Ligand excluded by PLIP D12.68: 6 residues within 4Å: Chain A: F.516 Chain B: L.207, R.208, I.209, F.211 Ligands: POV.83 Ligand excluded by PLIP D12.74: 4 residues within 4Å: Chain B: L.75, Y.78, L.80 Ligands: D10.75 Ligand excluded by PLIP D12.76: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP D12.78: 1 residues within 4Å: Chain B: P.298 Ligand excluded by PLIP D12.82: 2 residues within 4Å: Chain B: W.473 Ligands: POV.84 Ligand excluded by PLIP

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

LPE.5: 11 residues within 4Å: Chain A: I.199, L.202, A.203, I.206, P.339, T.341, P.342, I.394, V.398 Ligands: D12.4, D10.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.199, A:L.202, A:A.203, A:I.206, A:I.394, A:V.398 LPE.13: 10 residues within 4Å: Chain A: V.309, A.312, G.313, Y.316, V.435, I.439, F.441, L.442 Ligands: D10.11, D10.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.312, A:Y.316, A:Y.316, A:V.435, A:I.439, A:L.442, A:L.442, A:L.442 pi-Cation interactions: A:F.441 LPE.15: 5 residues within 4Å: Chain A: M.307, I.310, R.323, F.324 Ligands: LPE.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.310 Hydrogen bonds: A:R.323 LPE.16: 14 residues within 4Å: Chain A: I.270, A.271, V.274, T.275, I.278, M.307, I.310, A.311, V.314, F.320, R.323, F.324, K.325 Ligands: LPE.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.270, A:I.278, A:I.310, A:V.314, A:F.320, A:F.324 Salt bridges: A:K.325 LPE.22: 7 residues within 4Å: Chain A: K.256, M.485, I.488, L.493 Ligands: C14.23, CLR.42, POV.83 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.488, A:L.493 Salt bridges: A:K.256 LPE.25: 19 residues within 4Å: Chain A: K.158, I.209, F.211, V.212, Y.215, G.352, D.353, G.356, M.359, G.496, L.497, A.500, V.503 Chain B: L.508, F.512, Q.515 Ligands: POV.2, D10.24, C14.65 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:L.508, B:F.512, B:F.512, A:I.209, A:F.211, A:V.212, A:Y.215, A:Y.215, A:M.359, A:V.503 LPE.39: 7 residues within 4Å: Chain A: L.233, V.234, L.258, M.464, A.467 Ligands: D10.38, POV.40 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.233, A:V.234, A:L.258 LPE.46: 11 residues within 4Å: Chain B: I.199, L.202, A.203, I.206, P.339, T.341, P.342, I.394, V.398 Ligands: D12.45, D10.47 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.199, B:L.202, B:A.203, B:I.206, B:I.394, B:V.398 LPE.54: 13 residues within 4Å: Chain B: I.96, F.305, V.309, A.312, G.313, Y.316, V.435, F.441, L.442, L.443, P.445 Ligands: D10.52, D10.53 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.96, B:F.305, B:V.309, B:V.309, B:A.312, B:Y.316, B:Y.316, B:V.435, B:L.442, B:L.443, B:P.445 pi-Cation interactions: B:F.441 LPE.56: 3 residues within 4Å: Chain B: R.323 Ligands: LPE.57, D10.58 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.323, B:R.323 Salt bridges: B:R.323 LPE.57: 12 residues within 4Å: Chain B: I.270, A.271, T.275, I.278, M.307, I.310, A.311, V.314, F.320, F.324, K.325 Ligands: LPE.56 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.270, B:A.271, B:I.278, B:I.310, B:A.311, B:V.314, B:F.320, B:F.324, B:F.324 Salt bridges: B:K.325 LPE.64: 9 residues within 4Å: Chain B: V.252, K.256, M.485, I.488, V.492, L.493 Ligands: POV.2, CLR.63, C14.65 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.488, B:I.488, B:V.492, B:L.493 Salt bridges: B:K.256 LPE.67: 16 residues within 4Å: Chain A: F.512, Q.515 Chain B: I.209, F.211, V.212, Y.215, G.352, D.353, G.356, G.496, L.497, A.500, V.503 Ligands: C14.23, D10.66, POV.83 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.209, B:F.211, B:F.211, B:V.212, B:Y.215, B:Y.215, B:V.503, A:F.512 Hydrogen bonds: B:D.353 LPE.81: 3 residues within 4Å: Chain B: L.233, M.464 Ligands: POV.84 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.233

38 x D10: DECANE(Non-covalent)(Non-functional Binders)

D10.6: 3 residues within 4Å: Chain A: P.339, I.394 Ligands: LPE.5 Ligand excluded by PLIP D10.8: 2 residues within 4Å: Chain A: F.121, I.125 Ligand excluded by PLIP D10.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP D10.11: 3 residues within 4Å: Chain A: I.439 Ligands: D10.12, LPE.13 Ligand excluded by PLIP D10.12: 2 residues within 4Å: Ligands: D10.11, LPE.13 Ligand excluded by PLIP D10.14: 1 residues within 4Å: Chain A: V.309 Ligand excluded by PLIP D10.17: 1 residues within 4Å: Chain A: V.274 Ligand excluded by PLIP D10.18: 1 residues within 4Å: Chain A: L.277 Ligand excluded by PLIP D10.19: 1 residues within 4Å: Chain A: I.265 Ligand excluded by PLIP D10.20: 2 residues within 4Å: Chain A: I.265 Ligands: D12.21 Ligand excluded by PLIP D10.24: 7 residues within 4Å: Chain A: A.500, V.503, L.507 Chain B: A.504 Ligands: POV.2, LPE.25, C14.65 Ligand excluded by PLIP D10.27: 3 residues within 4Å: Chain A: I.64, L.68, R.208 Ligand excluded by PLIP D10.28: 1 residues within 4Å: Chain A: P.58 Ligand excluded by PLIP D10.29: 4 residues within 4Å: Chain A: V.65, L.66, F.69 Ligands: D10.30 Ligand excluded by PLIP D10.30: 4 residues within 4Å: Chain A: A.72, P.76, F.129 Ligands: D10.29 Ligand excluded by PLIP D10.31: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP D10.33: 5 residues within 4Å: Chain A: I.92, I.427, I.430, I.431 Ligands: D12.32 Ligand excluded by PLIP D10.37: 3 residues within 4Å: Chain A: L.277, L.280, S.284 Ligand excluded by PLIP D10.38: 4 residues within 4Å: Chain A: L.233, L.280, K.460 Ligands: LPE.39 Ligand excluded by PLIP D10.47: 1 residues within 4Å: Ligands: LPE.46 Ligand excluded by PLIP D10.49: 2 residues within 4Å: Chain B: F.121, I.125 Ligand excluded by PLIP D10.51: 1 residues within 4Å: Ligands: D10.52 Ligand excluded by PLIP D10.52: 4 residues within 4Å: Chain B: I.439 Ligands: D10.51, D10.53, LPE.54 Ligand excluded by PLIP D10.53: 2 residues within 4Å: Ligands: D10.52, LPE.54 Ligand excluded by PLIP D10.55: 1 residues within 4Å: Chain B: V.309 Ligand excluded by PLIP D10.58: 2 residues within 4Å: Chain B: V.274 Ligands: LPE.56 Ligand excluded by PLIP D10.59: 1 residues within 4Å: Chain B: L.277 Ligand excluded by PLIP D10.60: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP D10.61: 2 residues within 4Å: Chain B: F.262 Ligands: D12.62 Ligand excluded by PLIP D10.66: 5 residues within 4Å: Chain B: A.500, L.507 Ligands: C14.23, LPE.67, POV.83 Ligand excluded by PLIP D10.69: 2 residues within 4Å: Chain B: L.68, R.208 Ligand excluded by PLIP D10.70: 1 residues within 4Å: Chain B: P.58 Ligand excluded by PLIP D10.71: 6 residues within 4Å: Chain B: K.62, V.65, L.66, F.69, A.72 Ligands: D10.72 Ligand excluded by PLIP D10.72: 3 residues within 4Å: Chain B: L.75 Ligands: D10.71, D10.73 Ligand excluded by PLIP D10.73: 1 residues within 4Å: Ligands: D10.72 Ligand excluded by PLIP D10.75: 5 residues within 4Å: Chain B: I.88, I.427, I.430, I.431 Ligands: D12.74 Ligand excluded by PLIP D10.79: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP D10.80: 3 residues within 4Å: Chain B: L.233, L.280, L.456 Ligand excluded by PLIP

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.42: 7 residues within 4Å: Chain A: V.252, F.255, K.256, I.488, V.492 Ligands: D12.21, LPE.22 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.252, A:F.255, A:K.256, A:I.488, A:V.492 CLR.63: 5 residues within 4Å: Chain B: F.255, K.256, V.492 Ligands: D12.62, LPE.64 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.255, B:F.255, B:F.255, B:K.256, B:V.492

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X. et al., Cryo-EM structure of human DRA (SLC26A3) bound with oxalate. To Be Published

Release Date

2025-05-14

Peptides

Chloride anion exchanger: 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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Chloride anion exchanger

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