SMTL ID : 8qsl.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 15 residues within 4Å: Chain A: 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: Y01.2 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:F.417, B:A.541, B:L.548, A:A.418, A:I.421, A:K.425, A:W.453, A:L.460, A:L.460 Salt bridges: A:K.425, A:K.425 Y01.2: 7 residues within 4Å: Chain A: K.425 Chain B: Y.534, F.537, L.538, A.541 Ligands: Y01.1, PGT.16 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.534, B:L.538, B:A.541 Salt bridges: A:K.425 Y01.3: 9 residues within 4Å: Chain A: L.392, L.397, L.398, F.411, F.467 Chain B: L.548, I.552, V.555 Ligands: Y01.11 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.548, B:I.552, B:V.555, A:L.392, A:L.397, A:L.398, A:F.411, A:F.467 Salt bridges: A:K.403 Y01.5: 5 residues within 4Å: Chain A: D.448, S.450, W.452, W.453, V.455 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.452, A:W.453, A:W.453, A:W.453, A:V.455 Y01.6: 4 residues within 4Å: Chain A: F.501, V.502, S.504, G.505 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.502 Y01.7: 5 residues within 4Å: Chain A: P.323, L.326, A.327, V.502, L.549 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.326, A:V.502, A:L.549 Y01.9: 14 residues within 4Å: Chain A: F.417, A.541, G.544, A.545, L.548 Chain B: C.414, A.418, I.421, L.422, K.425, L.449, W.453, L.460 Ligands: Y01.10 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.418, B:I.421, B:K.425, B:W.453, B:L.460, B:L.460, A:F.417, A:A.541, A:L.548 Salt bridges: B:K.425 Y01.10: 7 residues within 4Å: Chain A: Y.534, F.537, L.538, A.541 Chain B: K.425 Ligands: PGT.8, Y01.9 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.534, A:L.538, A:A.541 Salt bridges: B:K.425 Y01.11: 11 residues within 4Å: Chain A: K.403, L.548, I.552, V.555 Chain B: L.392, L.397, L.398, K.403, F.411, F.467 Ligands: Y01.3 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.548, A:I.552, A:V.555, B:L.392, B:L.397, B:L.398, B:F.411, B:F.467 Salt bridges: B:K.403 Y01.13: 5 residues within 4Å: Chain B: D.448, S.450, W.452, W.453, V.455 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.452, B:W.453, B:W.453, B:V.455 Y01.14: 4 residues within 4Å: Chain B: F.501, V.502, S.504, G.505 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.502 Y01.15: 5 residues within 4Å: Chain B: P.323, L.326, A.327, V.502, L.549 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.326, B:V.502, B:L.549

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

NAG.4: 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.8: 4 residues within 4Å: Chain A: A.514, I.515, W.517 Ligands: Y01.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.515 PGT.16: 4 residues within 4Å: Chain B: A.514, I.515, W.517 Ligands: Y01.2 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.515

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 LMNG. To Be Published

Release Date

2023-10-25

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

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