SMTL ID : 8jkv.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: 6 residues within 4Å: Chain A: Y.98, F.109, Q.140, N.142, E.147, E.149 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: A.75, L.83, L.85, N.162, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: Y.98, F.109, Q.140, N.142, E.147, E.149 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain B: A.75, L.83, L.85, N.162, N.184 No protein-ligand interaction detected (PLIP)

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

NAG.5: 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:Q.117 NAG.41: 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:Q.117

6 x D12: DODECANE(Non-covalent)

D12.6: 4 residues within 4Å: Chain A: I.208, R.212, F.600 Ligands: R16.34 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.208, A:F.600 D12.23: 6 residues within 4Å: Chain A: C.351, I.355, L.366 Chain B: F.621, W.625 Ligands: OCT.24 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.621, B:W.625, A:I.355 D12.39: 3 residues within 4Å: Chain A: F.621, P.622, W.625 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.621, A:P.622, A:W.625, A:W.625 D12.40: 3 residues within 4Å: Chain B: F.621, P.622, W.625 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.621, B:P.622, B:W.625 D12.42: 4 residues within 4Å: Chain B: I.208, R.212, F.600 Ligands: R16.69 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.208, B:F.600 D12.59: 6 residues within 4Å: Chain A: F.621, W.625 Chain B: C.351, I.355, L.366 Ligands: OCT.38 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.621, A:W.625, B:I.355

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

OCT.7: 7 residues within 4Å: Chain A: F.617, F.621, P.622, F.623 Chain B: I.355, I.356 Ligands: OCT.60 Ligand excluded by PLIP OCT.8: 4 residues within 4Å: Chain A: K.529, I.533, T.536 Ligands: C14.28 Ligand excluded by PLIP OCT.14: 3 residues within 4Å: Chain A: F.394, L.422, L.423 Ligand excluded by PLIP OCT.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.18: 1 residues within 4Å: Chain A: F.436 Ligand excluded by PLIP OCT.21: 2 residues within 4Å: Chain A: L.474 Ligands: D10.22 Ligand excluded by PLIP OCT.24: 1 residues within 4Å: Ligands: D12.23 Ligand excluded by PLIP OCT.25: 4 residues within 4Å: Chain A: I.356, V.612 Chain B: F.617 Ligands: OCT.43 Ligand excluded by PLIP OCT.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.27: 3 residues within 4Å: Chain A: I.533, A.537, I.541 Ligand excluded by PLIP OCT.32: 2 residues within 4Å: Chain A: A.548 Ligands: C14.19 Ligand excluded by PLIP OCT.33: 4 residues within 4Å: Chain A: F.198, Y.294 Ligands: C14.31, OCT.36 Ligand excluded by PLIP OCT.35: 3 residues within 4Å: Chain A: A.197, F.198, G.201 Ligand excluded by PLIP OCT.36: 3 residues within 4Å: Chain A: L.281, I.581 Ligands: OCT.33 Ligand excluded by PLIP OCT.37: 2 residues within 4Å: Chain A: I.373, L.473 Ligand excluded by PLIP OCT.38: 1 residues within 4Å: Ligands: D12.59 Ligand excluded by PLIP OCT.43: 7 residues within 4Å: Chain A: I.355, I.356 Chain B: F.617, F.621, P.622, F.623 Ligands: OCT.25 Ligand excluded by PLIP OCT.44: 4 residues within 4Å: Chain B: K.529, I.533, T.536 Ligands: C14.63 Ligand excluded by PLIP OCT.50: 3 residues within 4Å: Chain B: F.394, L.422, L.423 Ligand excluded by PLIP OCT.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.54: 1 residues within 4Å: Chain B: F.436 Ligand excluded by PLIP OCT.57: 2 residues within 4Å: Chain B: L.474 Ligands: D10.58 Ligand excluded by PLIP OCT.60: 4 residues within 4Å: Chain A: F.617 Chain B: I.356, V.612 Ligands: OCT.7 Ligand excluded by PLIP OCT.61: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OCT.62: 3 residues within 4Å: Chain B: I.533, A.537, I.541 Ligand excluded by PLIP OCT.67: 2 residues within 4Å: Chain B: A.548 Ligands: C14.55 Ligand excluded by PLIP OCT.68: 4 residues within 4Å: Chain B: F.198, Y.294 Ligands: C14.66, OCT.71 Ligand excluded by PLIP OCT.70: 3 residues within 4Å: Chain B: A.197, F.198, G.201 Ligand excluded by PLIP OCT.71: 3 residues within 4Å: Chain B: L.281, I.581 Ligands: OCT.68 Ligand excluded by PLIP OCT.72: 2 residues within 4Å: Chain B: I.373, L.473 Ligand excluded by PLIP

24 x C14: TETRADECANE(Non-covalent)

C14.9: 6 residues within 4Å: Chain A: I.196, A.197, K.634, T.638, I.641, V.642 Ligand excluded by PLIP C14.10: 5 residues within 4Å: Chain A: A.343, F.347, I.350, F.385 Ligands: C14.11 Ligand excluded by PLIP C14.11: 4 residues within 4Å: Chain A: F.336, R.337, A.343 Ligands: C14.10 Ligand excluded by PLIP C14.12: 4 residues within 4Å: Chain A: K.335, F.336, L.339, L.393 Ligand excluded by PLIP C14.13: 3 residues within 4Å: Chain A: V.389, L.390, L.393 Ligand excluded by PLIP C14.15: 4 residues within 4Å: Chain A: L.434, I.501, I.505, I.508 Ligand excluded by PLIP C14.19: 7 residues within 4Å: Chain A: W.421, L.432, L.549, F.558, L.568 Ligands: C14.20, OCT.32 Ligand excluded by PLIP C14.20: 5 residues within 4Å: Chain A: R.412, I.414, T.415, W.418 Ligands: C14.19 Ligand excluded by PLIP C14.28: 5 residues within 4Å: Chain A: L.532, V.584, P.587, K.592 Ligands: OCT.8 Ligand excluded by PLIP C14.29: 6 residues within 4Å: Chain A: I.205, R.212, W.595, T.596, T.598, F.600 Ligand excluded by PLIP C14.30: 5 residues within 4Å: Chain A: G.302, L.303, C.539, S.576, F.580 Ligand excluded by PLIP C14.31: 4 residues within 4Å: Chain A: W.293, L.303, L.308 Ligands: OCT.33 Ligand excluded by PLIP C14.45: 6 residues within 4Å: Chain B: I.196, A.197, K.634, T.638, I.641, V.642 Ligand excluded by PLIP C14.46: 5 residues within 4Å: Chain B: A.343, F.347, I.350, F.385 Ligands: C14.47 Ligand excluded by PLIP C14.47: 4 residues within 4Å: Chain B: F.336, R.337, A.343 Ligands: C14.46 Ligand excluded by PLIP C14.48: 4 residues within 4Å: Chain B: K.335, F.336, L.339, L.393 Ligand excluded by PLIP C14.49: 3 residues within 4Å: Chain B: V.389, L.390, L.393 Ligand excluded by PLIP C14.51: 4 residues within 4Å: Chain B: L.434, I.501, I.505, I.508 Ligand excluded by PLIP C14.55: 7 residues within 4Å: Chain B: W.421, L.432, L.549, F.558, L.568 Ligands: C14.56, OCT.67 Ligand excluded by PLIP C14.56: 5 residues within 4Å: Chain B: R.412, I.414, T.415, W.418 Ligands: C14.55 Ligand excluded by PLIP C14.63: 5 residues within 4Å: Chain B: L.532, V.584, P.587, K.592 Ligands: OCT.44 Ligand excluded by PLIP C14.64: 6 residues within 4Å: Chain B: I.205, R.212, W.595, T.596, T.598, F.600 Ligand excluded by PLIP C14.65: 5 residues within 4Å: Chain B: G.302, L.303, C.539, S.576, F.580 Ligand excluded by PLIP C14.66: 4 residues within 4Å: Chain B: W.293, L.303, L.308 Ligands: OCT.68 Ligand excluded by PLIP

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.17: 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.53: 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)

D10.22: 3 residues within 4Å: Chain A: L.473, L.474 Ligands: OCT.21 No protein-ligand interaction detected (PLIP) D10.58: 3 residues within 4Å: Chain B: L.473, L.474 Ligands: OCT.57 No protein-ligand interaction detected (PLIP)

2 x R16: HEXADECANE(Non-covalent)

R16.34: 6 residues within 4Å: Chain A: L.281, P.599, T.644, V.648, Y.652 Ligands: D12.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.281, A:P.599, A:T.644, A:V.648, A:V.648, A:Y.652 R16.69: 6 residues within 4Å: Chain B: L.281, P.599, T.644, V.648, Y.652 Ligands: D12.42 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.281, B:P.599, B:T.644, B:V.648, 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.
Show / Hide

Heparan-alpha-glucosaminide N-acetyltransferase

Related Entries With Identical Sequence