SMTL ID : 8jl3.1

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)

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

NAG.5: 11 residues within 4Å: Chain A: N.286, H.297, A.306, V.309, F.310, R.372, Y.481, P.498, E.499, K.563 Ligands: ACO.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.309 Hydrogen bonds: A:N.286, A:N.286, A:H.297, A:R.372, A:R.372, A:K.563, A:K.563 NAG.7: 4 residues within 4Å: Chain A: W.92, N.94, Q.117, L.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.94 NAG.43: 11 residues within 4Å: Chain B: N.286, H.297, A.306, V.309, F.310, R.372, Y.481, P.498, E.499, K.563 Ligands: ACO.44 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.309 Hydrogen bonds: B:N.286, B:N.286, B:H.297, B:R.372, B:R.372, B:K.563, B:K.563 NAG.45: 4 residues within 4Å: Chain B: W.92, N.94, Q.117, L.145 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.94

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

ACO.6: 23 residues within 4Å: Chain A: R.267, L.268, V.271, D.272, R.275, M.282, F.310, F.313, I.316, 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 Ligands: NAG.5 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.376, A:L.380, A:I.608, A:Y.611 Hydrogen bonds: A:R.267, A:L.268, A:L.268, A:D.272, A:R.275, A:R.275, A:S.320, A:S.324, A:S.324, A:S.607, A:K.662 Salt bridges: A:R.275, A:R.275, A:K.341, A:R.345, A:R.345, A:K.662 pi-Cation interactions: A:R.267 ACO.44: 23 residues within 4Å: Chain B: R.267, L.268, V.271, D.272, R.275, M.282, F.310, F.313, I.316, 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 Ligands: NAG.43 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:V.376, B:L.380, B:I.608, B:Y.611 Hydrogen bonds: B:R.267, B:L.268, B:L.268, B:D.272, B:R.275, B:R.275, B:S.320, B:S.324, B:S.324, B:S.607, B:K.662 Salt bridges: B:R.275, B:R.275, B:K.341, B:R.345, B:R.345, B:K.662 pi-Cation interactions: B:R.267

6 x D12: DODECANE(Non-covalent)

D12.8: 2 residues within 4Å: Chain A: R.212 Ligands: R16.37 No protein-ligand interaction detected (PLIP) D12.26: 8 residues within 4Å: Chain A: I.355, L.366, S.367, W.368 Chain B: F.621, W.625, K.626 Ligands: D12.42 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.621, B:F.621, B:W.625, A:I.355, A:L.366, A:W.368 D12.41: 4 residues within 4Å: Chain A: F.621, P.622, W.625 Ligands: D12.64 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.621, A:P.622, A:W.625 D12.42: 4 residues within 4Å: Chain B: F.621, P.622, W.625 Ligands: D12.26 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.621, B:P.622, B:W.625 D12.46: 2 residues within 4Å: Chain B: R.212 Ligands: R16.75 No protein-ligand interaction detected (PLIP) D12.64: 8 residues within 4Å: Chain A: F.621, W.625, K.626 Chain B: I.355, L.366, S.367, W.368 Ligands: D12.41 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.355, B:L.366, B:W.368, A:F.621, A:W.625

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

OCT.9: 5 residues within 4Å: Chain A: L.609, F.617, F.621, P.622, F.623 Ligand excluded by PLIP OCT.10: 3 residues within 4Å: Chain A: W.418, L.422 Ligands: C14.23 Ligand excluded by PLIP OCT.11: 2 residues within 4Å: Chain A: T.536 Ligands: C14.31 Ligand excluded by PLIP OCT.17: 2 residues within 4Å: Chain A: F.394, L.423 Ligand excluded by PLIP OCT.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.21: 1 residues within 4Å: Chain A: G.429 Ligand excluded by PLIP OCT.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.27: 1 residues within 4Å: Chain A: W.368 Ligand excluded by PLIP OCT.28: 2 residues within 4Å: Chain A: I.356, V.612 Ligand excluded by PLIP OCT.29: 2 residues within 4Å: Ligands: C14.15, C14.16 Ligand excluded by PLIP OCT.30: 4 residues within 4Å: Chain A: L.409, L.411, W.538, I.541 Ligand excluded by PLIP OCT.35: 3 residues within 4Å: Chain A: A.548, F.558 Ligands: C14.22 Ligand excluded by PLIP OCT.36: 2 residues within 4Å: Chain A: Y.294 Ligands: OCT.39 Ligand excluded by PLIP OCT.38: 4 residues within 4Å: Chain A: A.197, G.201 Ligands: C14.12, R16.37 Ligand excluded by PLIP OCT.39: 6 residues within 4Å: Chain A: I.277, L.281, V.305, I.581 Ligands: C14.34, OCT.36 Ligand excluded by PLIP OCT.40: 4 residues within 4Å: Chain A: I.373, L.473, L.474, L.475 Ligand excluded by PLIP OCT.47: 5 residues within 4Å: Chain B: L.609, F.617, F.621, P.622, F.623 Ligand excluded by PLIP OCT.48: 3 residues within 4Å: Chain B: W.418, L.422 Ligands: C14.61 Ligand excluded by PLIP OCT.49: 2 residues within 4Å: Chain B: T.536 Ligands: C14.69 Ligand excluded by PLIP OCT.55: 2 residues within 4Å: Chain B: F.394, L.423 Ligand excluded by PLIP OCT.57: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.59: 1 residues within 4Å: Chain B: G.429 Ligand excluded by PLIP OCT.62: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.65: 1 residues within 4Å: Chain B: W.368 Ligand excluded by PLIP OCT.66: 2 residues within 4Å: Chain B: I.356, V.612 Ligand excluded by PLIP OCT.67: 2 residues within 4Å: Ligands: C14.53, C14.54 Ligand excluded by PLIP OCT.68: 4 residues within 4Å: Chain B: L.409, L.411, W.538, I.541 Ligand excluded by PLIP OCT.73: 3 residues within 4Å: Chain B: A.548, F.558 Ligands: C14.60 Ligand excluded by PLIP OCT.74: 2 residues within 4Å: Chain B: Y.294 Ligands: OCT.77 Ligand excluded by PLIP OCT.76: 4 residues within 4Å: Chain B: A.197, G.201 Ligands: C14.50, R16.75 Ligand excluded by PLIP OCT.77: 6 residues within 4Å: Chain B: I.277, L.281, V.305, I.581 Ligands: C14.72, OCT.74 Ligand excluded by PLIP OCT.78: 4 residues within 4Å: Chain B: I.373, L.473, L.474, L.475 Ligand excluded by PLIP

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

C14.12: 7 residues within 4Å: Chain A: P.193, I.196, K.634, T.638, I.641, V.642 Ligands: OCT.38 Ligand excluded by PLIP C14.13: 6 residues within 4Å: Chain A: G.340, A.343, S.346, F.347, I.350, F.385 Ligand excluded by PLIP C14.14: 3 residues within 4Å: Chain A: F.336, G.340, A.343 Ligand excluded by PLIP C14.15: 4 residues within 4Å: Chain A: S.334, K.335, F.336 Ligands: OCT.29 Ligand excluded by PLIP C14.16: 5 residues within 4Å: Chain A: V.386, V.389, L.393, L.423 Ligands: OCT.29 Ligand excluded by PLIP C14.18: 3 residues within 4Å: Chain A: L.473, I.501, I.505 Ligand excluded by PLIP C14.22: 6 residues within 4Å: Chain A: W.421, L.432, F.558, L.568 Ligands: C14.23, OCT.35 Ligand excluded by PLIP C14.23: 6 residues within 4Å: Chain A: I.414, T.415, W.418, W.421 Ligands: OCT.10, C14.22 Ligand excluded by PLIP C14.31: 2 residues within 4Å: Chain A: L.532 Ligands: OCT.11 Ligand excluded by PLIP C14.32: 7 residues within 4Å: Chain A: S.209, R.212, L.594, W.595, T.596, T.598, F.600 Ligand excluded by PLIP C14.33: 4 residues within 4Å: Chain A: C.539, T.573, F.577, F.580 Ligand excluded by PLIP C14.34: 1 residues within 4Å: Ligands: OCT.39 Ligand excluded by PLIP C14.50: 7 residues within 4Å: Chain B: P.193, I.196, K.634, T.638, I.641, V.642 Ligands: OCT.76 Ligand excluded by PLIP C14.51: 6 residues within 4Å: Chain B: G.340, A.343, S.346, F.347, I.350, F.385 Ligand excluded by PLIP C14.52: 3 residues within 4Å: Chain B: F.336, G.340, A.343 Ligand excluded by PLIP C14.53: 4 residues within 4Å: Chain B: S.334, K.335, F.336 Ligands: OCT.67 Ligand excluded by PLIP C14.54: 5 residues within 4Å: Chain B: V.386, V.389, L.393, L.423 Ligands: OCT.67 Ligand excluded by PLIP C14.56: 3 residues within 4Å: Chain B: L.473, I.501, I.505 Ligand excluded by PLIP C14.60: 6 residues within 4Å: Chain B: W.421, L.432, F.558, L.568 Ligands: C14.61, OCT.73 Ligand excluded by PLIP C14.61: 6 residues within 4Å: Chain B: I.414, T.415, W.418, W.421 Ligands: OCT.48, C14.60 Ligand excluded by PLIP C14.69: 2 residues within 4Å: Chain B: L.532 Ligands: OCT.49 Ligand excluded by PLIP C14.70: 7 residues within 4Å: Chain B: S.209, R.212, L.594, W.595, T.596, T.598, F.600 Ligand excluded by PLIP C14.71: 4 residues within 4Å: Chain B: C.539, T.573, F.577, F.580 Ligand excluded by PLIP C14.72: 1 residues within 4Å: Ligands: OCT.77 Ligand excluded by PLIP

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.20: 7 residues within 4Å: Chain A: V.426, G.429, L.430, G.433, L.434, L.437, P.439 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.426, A:L.434, A:L.437, A:L.437 CLR.58: 7 residues within 4Å: Chain B: V.426, G.429, L.430, G.433, L.434, L.437, P.439 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.426, B:L.434, B:L.437, B:L.437

2 x D10: DECANE(Non-covalent)

D10.25: 2 residues within 4Å: Chain A: L.473, L.474 No protein-ligand interaction detected (PLIP) D10.63: 2 residues within 4Å: Chain B: L.473, L.474 No protein-ligand interaction detected (PLIP)

2 x R16: HEXADECANE(Non-covalent)

R16.37: 7 residues within 4Å: Chain A: F.284, T.644, A.645, V.648, Y.652 Ligands: D12.8, OCT.38 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.284, A:T.644, A:V.648, A:Y.652, A:Y.652 R16.75: 7 residues within 4Å: Chain B: F.284, T.644, A.645, V.648, Y.652 Ligands: D12.46, OCT.76 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.284, B:T.644, B:V.648, B:Y.652, 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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