SMTL ID : 8qsk.1

Cryo-EM structure of human SLC15A4 dimer in outward open state in MSP1D1 nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 16 residues within 4Å: Chain A: F.410, C.414, A.418, I.421, L.422, K.425, L.449, W.453, L.460 Chain B: F.417, F.537, A.541, G.544, A.545, L.548 Ligands: Y01.9 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.410, A:A.418, A:I.421, A:K.425, A:W.453, A:L.460, B:F.417, B:F.537, B:A.541, B:L.548 Salt bridges: A:K.425 Y01.2: 12 residues within 4Å: Chain A: L.380, L.398, K.403, V.407, I.466, F.467 Chain B: K.403, L.548, L.551, I.552, V.555 Ligands: Y01.11 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:L.548, B:L.548, B:L.551, B:I.552, B:V.555, A:L.380, A:L.398, A:V.407, A:I.466, A:F.467, A:F.467 Salt bridges: B:K.403, A:K.403 Y01.4: 7 residues within 4Å: Chain A: D.448, S.450, W.452, W.453, V.455, P.456 Ligands: Y01.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.452, A:W.453, A:W.453, A:V.455, A:P.456 Y01.5: 4 residues within 4Å: Chain A: F.501, V.502, S.504, G.505 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.501, A:V.502 Y01.6: 8 residues within 4Å: Chain A: P.323, L.326, A.327, P.330, V.502, L.549, I.553 Ligands: PGT.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.323, A:L.326, A:P.330, A:V.502, A:I.553 Y01.8: 9 residues within 4Å: Chain A: Y.534, F.537, L.538, A.541, I.542 Chain B: K.425 Ligands: PGT.7, Y01.10, Y01.13 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:K.425 Hydrophobic interactions: A:Y.534, A:Y.534, A:L.538, A:A.541 Y01.9: 10 residues within 4Å: Chain A: K.425, W.453 Chain B: Y.534, F.537, L.538, A.541, I.542 Ligands: Y01.1, Y01.4, PGT.16 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.453, B:Y.534, B:Y.534, B:L.538, B:A.541, B:I.542 Salt bridges: A:K.425 Y01.10: 16 residues within 4Å: Chain A: F.417, F.537, A.541, G.544, A.545, L.548 Chain B: F.410, C.414, A.418, I.421, L.422, K.425, L.449, W.453, L.460 Ligands: Y01.8 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.410, B:A.418, B:I.421, B:K.425, B:W.453, B:L.460, A:F.417, A:A.541, A:L.548 Salt bridges: B:K.425 Y01.11: 13 residues within 4Å: Chain A: K.403, L.548, L.551, I.552, V.555 Chain B: L.380, L.398, K.403, F.411, I.463, I.466, F.467 Ligands: Y01.2 16 PLIP interactions: 8 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:L.380, B:L.398, B:F.411, B:I.463, B:I.466, B:F.467, B:F.467, A:L.548, A:L.548, A:L.551, A:I.552, A:I.552, A:V.555 Salt bridges: B:K.403, A:K.403, A:K.403 Y01.13: 7 residues within 4Å: Chain B: D.448, S.450, W.452, W.453, V.455, P.456 Ligands: Y01.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.452, B:W.453, B:W.453, B:V.455, B:P.456 Y01.14: 4 residues within 4Å: Chain B: F.501, V.502, S.504, G.505 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.501, B:V.502 Y01.15: 8 residues within 4Å: Chain B: P.323, L.326, A.327, P.330, V.502, L.549, I.553 Ligands: PGT.16 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.323, B:L.326, B:P.330, B:V.502, B:I.553

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

NAG.3: 3 residues within 4Å: Chain A: P.66, L.138, N.140 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.66 NAG.12: 3 residues within 4Å: Chain B: P.66, L.138, N.140 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.66

2 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.7: 8 residues within 4Å: Chain A: A.514, I.515, W.517, Y.531, Y.534, L.538 Ligands: Y01.6, Y01.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.515, A:W.517, A:L.538 PGT.16: 6 residues within 4Å: Chain B: A.514, I.515, W.517, L.538 Ligands: Y01.9, Y01.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.515, B:L.538

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rehan, S. et al., Cryo-EM structure of human SLC15A4 dimer in outward open state in MSP1D1 nanodisc. To Be Published

Release Date

2023-11-01

Peptides

Solute carrier family 15 member 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Membrane

We predict this structure to be a membrane protein.
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Solute carrier family 15 member 4