SMTL ID : 8w4a.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: 4 residues within 4Å: Chain B: E.76, L.83, N.162, N.184 No protein-ligand interaction detected (PLIP)

2 x UV6: ~{N}-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-2-[[(2~{R},4~{R})-4-methyl-2-oxidanyl-3,4-dihydro-2~{H}-chromen-7-yl]oxy]-4,5-bis(oxidanyl)oxan-3-yl]ethanamide(Non-covalent)

UV6.5: 16 residues within 4Å: Chain A: V.285, N.286, Y.287, H.297, A.306, V.309, F.310, R.372, Y.481, P.498, E.499, K.563, H.614, E.615, E.618 Ligands: ACO.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.285, A:V.309 Hydrogen bonds: A:N.286, A:H.297, A:R.372, A:R.372, A:E.499, A:K.563, A:E.618, A:E.618 Salt bridges: A:H.297, A:H.614 UV6.45: 16 residues within 4Å: Chain B: V.285, N.286, Y.287, H.297, A.306, V.309, F.310, R.372, Y.481, P.498, E.499, K.563, H.614, E.615, E.618 Ligands: ACO.46 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.285, B:V.309 Hydrogen bonds: B:N.286, B:H.297, B:R.372, B:R.372, B:E.499, B:K.563, B:E.618, B:E.618 Salt bridges: B:H.297, B:H.614

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

ACO.6: 24 residues within 4Å: Chain A: R.267, L.268, V.271, D.272, R.275, M.282, N.286, 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: UV6.5 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.376, A:L.380, A:Y.611 Hydrogen bonds: A:R.267, A:R.267, A:L.268, A:D.272, A:D.272, A:R.275, A:R.275, A:F.313, A:S.320, 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.46: 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: UV6.45 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:V.376, B:I.608, B:Y.611 Hydrogen bonds: B:R.267, B:L.268, B:D.272, B:D.272, B:R.275, B:R.275, B:S.320, 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

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

NAG.7: 3 residues within 4Å: Chain A: W.92, N.94, Q.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.117, A:Q.117 NAG.47: 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:Q.117

24 x C14: TETRADECANE(Non-covalent)

C14.8: 5 residues within 4Å: Chain A: G.340, A.343, F.347, I.350, F.385 Ligand excluded by PLIP C14.9: 5 residues within 4Å: Chain A: S.334, F.336, R.337, G.340, A.343 Ligand excluded by PLIP C14.10: 5 residues within 4Å: Chain A: K.335, F.336, V.389, L.393 Ligands: OCT.27 Ligand excluded by PLIP C14.11: 5 residues within 4Å: Chain A: V.389, L.393, F.394, L.423 Ligands: OCT.27 Ligand excluded by PLIP C14.13: 4 residues within 4Å: Chain A: I.470, I.501, T.504, I.505 Ligand excluded by PLIP C14.17: 3 residues within 4Å: Chain A: L.549, F.558, L.568 Ligand excluded by PLIP C14.18: 6 residues within 4Å: Chain A: I.414, T.415, W.418, W.421, W.538 Ligands: OCT.42 Ligand excluded by PLIP C14.25: 9 residues within 4Å: Chain A: F.617, Y.620, F.621, F.623, K.657 Chain B: W.661 Ligands: OCT.24, HP6.26, OCT.64 Ligand excluded by PLIP C14.29: 4 residues within 4Å: Chain A: L.532, P.587, K.592 Ligands: D12.30 Ligand excluded by PLIP C14.32: 9 residues within 4Å: Chain A: I.205, R.212, G.593, L.594, W.595, T.596, T.598, F.600 Ligands: CLR.31 Ligand excluded by PLIP C14.33: 4 residues within 4Å: Chain A: L.303, C.539, S.576, F.577 Ligand excluded by PLIP C14.34: 2 residues within 4Å: Chain A: L.308, F.577 Ligand excluded by PLIP C14.48: 5 residues within 4Å: Chain B: G.340, A.343, F.347, I.350, F.385 Ligand excluded by PLIP C14.49: 5 residues within 4Å: Chain B: S.334, F.336, R.337, G.340, A.343 Ligand excluded by PLIP C14.50: 4 residues within 4Å: Chain B: K.335, F.336, V.389 Ligands: OCT.67 Ligand excluded by PLIP C14.51: 4 residues within 4Å: Chain B: V.389, L.393, L.423 Ligands: OCT.67 Ligand excluded by PLIP C14.53: 4 residues within 4Å: Chain B: I.501, T.504, I.505 Ligands: OCT.59 Ligand excluded by PLIP C14.57: 4 residues within 4Å: Chain B: L.549, F.558, L.568 Ligands: OCT.75 Ligand excluded by PLIP C14.58: 5 residues within 4Å: Chain B: I.414, T.415, W.418, W.421 Ligands: OCT.82 Ligand excluded by PLIP C14.65: 9 residues within 4Å: Chain A: W.661 Chain B: F.617, Y.620, F.621, F.623, K.657 Ligands: OCT.24, OCT.64, HP6.66 Ligand excluded by PLIP C14.69: 5 residues within 4Å: Chain B: T.528, L.532, P.587, K.592 Ligands: D12.70 Ligand excluded by PLIP C14.72: 8 residues within 4Å: Chain B: I.205, R.212, G.593, L.594, W.595, T.596, T.598 Ligands: CLR.71 Ligand excluded by PLIP C14.73: 4 residues within 4Å: Chain B: C.539, T.573, S.576, F.577 Ligand excluded by PLIP C14.74: 4 residues within 4Å: Chain B: T.304, L.308, W.312, F.577 Ligand excluded by PLIP

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

OCT.12: 1 residues within 4Å: Chain A: L.423 Ligand excluded by PLIP OCT.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.16: 1 residues within 4Å: Chain A: F.436 Ligand excluded by PLIP OCT.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.22: 2 residues within 4Å: Ligands: D12.21, D12.44 Ligand excluded by PLIP OCT.23: 3 residues within 4Å: Chain A: I.356, V.612 Chain B: F.617 Ligand excluded by PLIP OCT.24: 7 residues within 4Å: Chain A: L.609, I.659, F.660, W.661 Ligands: C14.25, OCT.64, C14.65 Ligand excluded by PLIP OCT.27: 3 residues within 4Å: Chain A: L.393 Ligands: C14.10, C14.11 Ligand excluded by PLIP OCT.28: 4 residues within 4Å: Chain A: C.408, I.533, W.538, I.541 Ligand excluded by PLIP OCT.35: 2 residues within 4Å: Chain A: A.548, L.549 Ligand excluded by PLIP OCT.36: 3 residues within 4Å: Chain A: R.156, W.293, Y.294 Ligand excluded by PLIP OCT.38: 6 residues within 4Å: Chain A: A.197, F.198, G.201, I.641 Ligands: R16.37, OCT.39 Ligand excluded by PLIP OCT.39: 5 residues within 4Å: Chain A: P.193, I.196, K.634, T.638 Ligands: OCT.38 Ligand excluded by PLIP OCT.40: 3 residues within 4Å: Chain A: L.281, W.312, I.581 Ligand excluded by PLIP OCT.41: 3 residues within 4Å: Chain A: I.373, L.474, L.475 Ligand excluded by PLIP OCT.42: 2 residues within 4Å: Chain A: T.415 Ligands: C14.18 Ligand excluded by PLIP OCT.52: 2 residues within 4Å: Chain B: L.422, L.423 Ligand excluded by PLIP OCT.54: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.56: 1 residues within 4Å: Chain B: F.436 Ligand excluded by PLIP OCT.59: 1 residues within 4Å: Ligands: C14.53 Ligand excluded by PLIP OCT.62: 2 residues within 4Å: Chain B: W.368 Ligands: D12.61 Ligand excluded by PLIP OCT.63: 3 residues within 4Å: Chain A: F.617 Chain B: I.356, V.612 Ligand excluded by PLIP OCT.64: 7 residues within 4Å: Chain B: L.609, I.659, F.660, W.661 Ligands: OCT.24, C14.25, C14.65 Ligand excluded by PLIP OCT.67: 2 residues within 4Å: Ligands: C14.50, C14.51 Ligand excluded by PLIP OCT.68: 5 residues within 4Å: Chain B: C.408, L.411, A.537, W.538, I.541 Ligand excluded by PLIP OCT.75: 1 residues within 4Å: Ligands: C14.57 Ligand excluded by PLIP OCT.76: 3 residues within 4Å: Chain B: R.156, N.191, Y.294 Ligand excluded by PLIP OCT.78: 5 residues within 4Å: Chain B: A.197, F.198, I.641 Ligands: R16.77, OCT.79 Ligand excluded by PLIP OCT.79: 5 residues within 4Å: Chain B: P.193, I.196, K.634, T.638 Ligands: OCT.78 Ligand excluded by PLIP OCT.80: 2 residues within 4Å: Chain B: W.312, I.581 Ligand excluded by PLIP OCT.81: 3 residues within 4Å: Chain B: I.373, L.474, L.475 Ligand excluded by PLIP OCT.82: 2 residues within 4Å: Chain B: T.415 Ligands: C14.58 Ligand excluded by PLIP

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.15: 7 residues within 4Å: Chain A: V.426, L.430, G.433, L.434, L.437, L.438, P.439 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.426, A:L.434, A:L.437, A:L.437, A:L.438 CLR.31: 6 residues within 4Å: Chain A: R.212, V.584, V.588, L.594, W.595 Ligands: C14.32 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.584, A:L.594, A:W.595, A:W.595 CLR.55: 7 residues within 4Å: Chain B: V.426, L.430, G.433, L.434, L.437, L.438, P.439 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.426, B:L.434, B:L.437, B:L.437, B:L.438, B:P.439 CLR.71: 6 residues within 4Å: Chain B: R.212, V.584, V.588, L.594, W.595 Ligands: C14.72 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.584, B:L.594, B:W.595, B:W.595, B:W.595, B:W.595

2 x D10: DECANE(Non-covalent)

D10.20: 1 residues within 4Å: Chain A: L.474 No protein-ligand interaction detected (PLIP) D10.60: 2 residues within 4Å: Chain B: L.473, L.474 No protein-ligand interaction detected (PLIP)

6 x D12: DODECANE(Non-covalent)

D12.21: 7 residues within 4Å: Chain A: L.366, S.367, W.368 Chain B: F.621, K.626 Ligands: OCT.22, D12.44 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.621, A:L.366 D12.30: 4 residues within 4Å: Chain A: K.529, L.532, T.536 Ligands: C14.29 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.529, A:L.532, A:L.532 D12.43: 4 residues within 4Å: Chain A: F.621, P.622, W.625 Ligands: D12.61 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.621, A:W.625, A:W.625, A:W.625 D12.44: 5 residues within 4Å: Chain B: F.621, P.622, W.625 Ligands: D12.21, OCT.22 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.621, B:P.622, B:W.625 D12.61: 7 residues within 4Å: Chain A: F.621, K.626 Chain B: I.355, L.366, W.368 Ligands: D12.43, OCT.62 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.366, B:W.368, A:F.621 D12.70: 4 residues within 4Å: Chain B: K.529, L.532, T.536 Ligands: C14.69 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.529, B:L.532, B:L.532

2 x HP6: HEPTANE(Non-covalent)

HP6.26: 4 residues within 4Å: Chain A: I.650, I.653, K.657 Ligands: C14.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.650, A:I.653 HP6.66: 2 residues within 4Å: Chain B: K.657 Ligands: C14.65 No protein-ligand interaction detected (PLIP)

2 x R16: HEXADECANE(Non-covalent)

R16.37: 2 residues within 4Å: Chain A: V.648 Ligands: OCT.38 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.648 R16.77: 4 residues within 4Å: Chain B: F.284, V.648, Y.652 Ligands: OCT.78 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.284, 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

2024-10-23

Peptides

Heparan-alpha-glucosaminide N-acetyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Membrane

We predict this structure to be a membrane protein.
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Heparan-alpha-glucosaminide N-acetyltransferase

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