SMTL ID : 8jl1.1

membrane proteins

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 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: 7 residues within 4Å: Chain A: Y.98, F.109, Q.140, N.142, E.147, K.148, E.149 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: L.83, N.162, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain B: Y.98, F.109, Q.140, N.142, E.147, K.148, E.149 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: L.83, N.162, N.184 No protein-ligand interaction detected (PLIP)

2 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.5: 25 residues within 4Å: Chain A: P.266, R.267, L.268, V.271, D.272, R.275, M.282, N.286, H.297, V.309, F.310, F.313, M.317, S.320, L.323, S.324, I.328, K.341, R.345, V.376, L.380, S.607, I.608, Y.611, K.662 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.309, A:F.310, A:V.376, A:I.608 Hydrogen bonds: A:R.267, A:L.268, A:D.272, A:D.272, A:R.275, A:R.275, A:N.286, A:F.313, A:S.320, A:S.324 Salt bridges: A:R.275, A:R.275, A:K.341, A:R.345, A:R.345 pi-Cation interactions: A:R.267 ACO.42: 25 residues within 4Å: Chain B: P.266, R.267, L.268, V.271, D.272, R.275, M.282, N.286, H.297, V.309, F.310, F.313, M.317, S.320, L.323, S.324, I.328, K.341, R.345, V.376, L.380, S.607, I.608, Y.611, K.662 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:V.309, B:F.310, B:V.376, B:I.608 Hydrogen bonds: B:R.267, B:L.268, B:D.272, B:D.272, B:R.275, B:R.275, B:N.286, B:F.313, B:S.320, B:S.324 Salt bridges: B:R.275, B:R.275, B:K.341, B:R.345, B:R.345 pi-Cation interactions: B:R.267

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

NAG.6: 4 residues within 4Å: Chain A: W.92, N.94, Q.117, L.145 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.94 NAG.43: 4 residues within 4Å: Chain B: W.92, N.94, Q.117, L.145 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.145 Hydrogen bonds: B:N.94

6 x D12: DODECANE(Non-covalent)

D12.7: 5 residues within 4Å: Chain A: I.208, R.212 Ligands: C14.31, R16.36, OCT.37 No protein-ligand interaction detected (PLIP) D12.25: 6 residues within 4Å: Chain A: C.351, L.366, W.368 Chain B: F.621, W.625 Ligands: D12.41 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.621, B:W.625, A:L.366, A:W.368, A:W.368 D12.40: 4 residues within 4Å: Chain A: F.621, P.622, W.625 Ligands: D12.62 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.621, A:P.622, A:W.625 D12.41: 4 residues within 4Å: Chain B: F.621, P.622, W.625 Ligands: D12.25 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.621, B:P.622, B:W.625 D12.44: 5 residues within 4Å: Chain B: I.208, R.212 Ligands: C14.68, R16.73, OCT.74 No protein-ligand interaction detected (PLIP) D12.62: 6 residues within 4Å: Chain A: F.621, W.625 Chain B: C.351, L.366, W.368 Ligands: D12.40 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.621, A:W.625, B:L.366, B:W.368, B:W.368

32 x OCT: N-OCTANE(Non-covalent)(Non-functional Binders)

OCT.8: 3 residues within 4Å: Chain A: F.617, F.623 Chain B: I.356 Ligand excluded by PLIP OCT.9: 3 residues within 4Å: Chain A: W.418, L.422 Ligands: C14.22 Ligand excluded by PLIP OCT.10: 3 residues within 4Å: Chain A: T.536, L.583 Ligands: C14.30 Ligand excluded by PLIP OCT.16: 3 residues within 4Å: Chain A: W.418, P.419, L.423 Ligand excluded by PLIP OCT.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.20: 1 residues within 4Å: Chain A: G.429 Ligand excluded by PLIP OCT.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.26: 1 residues within 4Å: Chain A: W.368 Ligand excluded by PLIP OCT.27: 3 residues within 4Å: Chain A: I.356, G.613 Chain B: F.617 Ligand excluded by PLIP OCT.28: 2 residues within 4Å: Ligands: C14.14, C14.15 Ligand excluded by PLIP OCT.29: 3 residues within 4Å: Chain A: L.409, W.538, I.541 Ligand excluded by PLIP OCT.34: 2 residues within 4Å: Chain A: A.548 Ligands: C14.21 Ligand excluded by PLIP OCT.35: 3 residues within 4Å: Chain A: Y.294, V.305 Ligands: OCT.38 Ligand excluded by PLIP OCT.37: 4 residues within 4Å: Chain A: A.197, G.201 Ligands: D12.7, C14.11 Ligand excluded by PLIP OCT.38: 5 residues within 4Å: Chain A: I.277, L.281, I.581 Ligands: C14.33, OCT.35 Ligand excluded by PLIP OCT.39: 3 residues within 4Å: Chain A: I.373, L.474, L.475 Ligand excluded by PLIP OCT.45: 3 residues within 4Å: Chain A: I.356 Chain B: F.617, F.623 Ligand excluded by PLIP OCT.46: 3 residues within 4Å: Chain B: W.418, L.422 Ligands: C14.59 Ligand excluded by PLIP OCT.47: 3 residues within 4Å: Chain B: T.536, L.583 Ligands: C14.67 Ligand excluded by PLIP OCT.53: 3 residues within 4Å: Chain B: W.418, P.419, L.423 Ligand excluded by PLIP OCT.55: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.57: 1 residues within 4Å: Chain B: G.429 Ligand excluded by PLIP OCT.60: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.63: 1 residues within 4Å: Chain B: W.368 Ligand excluded by PLIP OCT.64: 3 residues within 4Å: Chain A: F.617 Chain B: I.356, G.613 Ligand excluded by PLIP OCT.65: 2 residues within 4Å: Ligands: C14.51, C14.52 Ligand excluded by PLIP OCT.66: 3 residues within 4Å: Chain B: L.409, W.538, I.541 Ligand excluded by PLIP OCT.71: 2 residues within 4Å: Chain B: A.548 Ligands: C14.58 Ligand excluded by PLIP OCT.72: 3 residues within 4Å: Chain B: Y.294, V.305 Ligands: OCT.75 Ligand excluded by PLIP OCT.74: 4 residues within 4Å: Chain B: A.197, G.201 Ligands: D12.44, C14.48 Ligand excluded by PLIP OCT.75: 5 residues within 4Å: Chain B: I.277, L.281, I.581 Ligands: C14.70, OCT.72 Ligand excluded by PLIP OCT.76: 3 residues within 4Å: Chain B: I.373, L.474, L.475 Ligand excluded by PLIP

24 x C14: TETRADECANE(Non-covalent)(Non-functional Binders)

C14.11: 7 residues within 4Å: Chain A: P.193, I.196, K.634, T.638, I.641, V.642 Ligands: OCT.37 Ligand excluded by PLIP C14.12: 6 residues within 4Å: Chain A: G.340, A.343, S.346, F.347, F.385 Ligands: C14.13 Ligand excluded by PLIP C14.13: 3 residues within 4Å: Chain A: F.336, A.343 Ligands: C14.12 Ligand excluded by PLIP C14.14: 4 residues within 4Å: Chain A: K.335, F.336, V.389 Ligands: OCT.28 Ligand excluded by PLIP C14.15: 6 residues within 4Å: Chain A: V.389, L.390, L.393, F.394, L.423 Ligands: OCT.28 Ligand excluded by PLIP C14.17: 3 residues within 4Å: Chain A: L.434, L.473, I.501 Ligand excluded by PLIP C14.21: 5 residues within 4Å: Chain A: L.432, F.558, L.568 Ligands: C14.22, OCT.34 Ligand excluded by PLIP C14.22: 6 residues within 4Å: Chain A: I.414, T.415, W.418, W.421 Ligands: OCT.9, C14.21 Ligand excluded by PLIP C14.30: 4 residues within 4Å: Chain A: F.580, V.584, P.587 Ligands: OCT.10 Ligand excluded by PLIP C14.31: 8 residues within 4Å: Chain A: I.205, S.209, R.212, W.595, T.596, T.598, F.600 Ligands: D12.7 Ligand excluded by PLIP C14.32: 3 residues within 4Å: Chain A: S.576, F.577, F.580 Ligand excluded by PLIP C14.33: 1 residues within 4Å: Ligands: OCT.38 Ligand excluded by PLIP C14.48: 7 residues within 4Å: Chain B: P.193, I.196, K.634, T.638, I.641, V.642 Ligands: OCT.74 Ligand excluded by PLIP C14.49: 6 residues within 4Å: Chain B: G.340, A.343, S.346, F.347, F.385 Ligands: C14.50 Ligand excluded by PLIP C14.50: 3 residues within 4Å: Chain B: F.336, A.343 Ligands: C14.49 Ligand excluded by PLIP C14.51: 4 residues within 4Å: Chain B: K.335, F.336, V.389 Ligands: OCT.65 Ligand excluded by PLIP C14.52: 6 residues within 4Å: Chain B: V.389, L.390, L.393, F.394, L.423 Ligands: OCT.65 Ligand excluded by PLIP C14.54: 3 residues within 4Å: Chain B: L.434, L.473, I.501 Ligand excluded by PLIP C14.58: 5 residues within 4Å: Chain B: L.432, F.558, L.568 Ligands: C14.59, OCT.71 Ligand excluded by PLIP C14.59: 6 residues within 4Å: Chain B: I.414, T.415, W.418, W.421 Ligands: OCT.46, C14.58 Ligand excluded by PLIP C14.67: 4 residues within 4Å: Chain B: F.580, V.584, P.587 Ligands: OCT.47 Ligand excluded by PLIP C14.68: 8 residues within 4Å: Chain B: I.205, S.209, R.212, W.595, T.596, T.598, F.600 Ligands: D12.44 Ligand excluded by PLIP C14.69: 3 residues within 4Å: Chain B: S.576, F.577, F.580 Ligand excluded by PLIP C14.70: 1 residues within 4Å: Ligands: OCT.75 Ligand excluded by PLIP

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.19: 6 residues within 4Å: Chain A: G.429, L.430, G.433, L.434, L.437, P.439 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.430, A:L.434, A:L.437, A:L.437 CLR.56: 6 residues within 4Å: Chain B: G.429, L.430, G.433, L.434, L.437, P.439 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.430, B:L.434, B:L.437, B:L.437

2 x D10: DECANE(Non-covalent)

D10.24: 2 residues within 4Å: Chain A: L.473, L.474 No protein-ligand interaction detected (PLIP) D10.61: 2 residues within 4Å: Chain B: L.473, L.474 No protein-ligand interaction detected (PLIP)

2 x R16: HEXADECANE(Non-covalent)

R16.36: 5 residues within 4Å: Chain A: I.641, T.644, V.648, Y.652 Ligands: D12.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.641, A:T.644, A:V.648, A:Y.652 R16.73: 5 residues within 4Å: Chain B: I.641, T.644, V.648, Y.652 Ligands: D12.44 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.641, B:T.644, B:V.648, B:Y.652

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, R. et al., Structure and mechanism of lysosome transmembrane acetylation by HGSNAT. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-05-22

Peptides

Heparan-alpha-glucosaminide N-acetyltransferase: 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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Heparan-alpha-glucosaminide N-acetyltransferase

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