SMTL ID : 7pvn.1 (1 other biounit)

Crystal Structure of Human UBA6 in Complex with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 29 residues within 4Å: Chain A: R.46, V.466, G.467, C.468, G.469, A.470, T.496, D.497, P.498, D.499, S.504, N.505, R.508, Q.509, K.521, N.543, K.544, V.545, C.546, A.567, L.568, D.569, N.570, A.573, K.851, I.890, I.891 Ligands: MG.6, CA.8 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.470, A:D.497, A:D.497, A:N.505, A:Q.509, A:K.521, A:V.545, A:V.545, A:D.569, A:N.570 Salt bridges: A:R.46, A:R.508, A:R.508, A:K.521, A:K.521, A:K.851

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: E.420, A.421, A.422, D.423, L.904, L.907, E.908, K.911, K.922, F.935 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.420, A:D.423, A:D.423, A:E.908, A:E.908, A:K.911 GOL.3: 7 residues within 4Å: Chain A: E.94, K.95, C.96, Q.97, W.99, D.100, R.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.95, A:R.118 Water bridges: A:D.100 GOL.4: 11 residues within 4Å: Chain A: V.50, T.209, G.210, E.211, F.410, M.594, G.595, T.596, K.597, N.927, A.929 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.211, A:T.596, A:T.596, A:K.597, A:N.927, A:N.927 GOL.5: 9 residues within 4Å: Chain A: C.311, L.312, I.313, V.314, D.315, P.322, W.416, L.417, Y.418 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.312, A:L.312, A:V.314, A:Y.418 Water bridges: A:D.315

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: D.569 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.569, H2O.2, H2O.3

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 3 residues within 4Å: Chain A: A.422, D.423, E.426 No protein-ligand interaction detected (PLIP) CA.8: 6 residues within 4Å: Chain A: D.499, L.500, E.502, N.505, K.521 Ligands: ATP.1 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 5 residues within 4Å: Chain A: K.644, K.652, K.706, K.709, Y.710 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Truongvan, N. et al., Structures of UBA6 explain its dual specificity for ubiquitin and FAT10. Nat Commun (2022)

Release Date

2022-08-31

Peptides

Ubiquitin-like modifier-activating enzyme 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ubiquitin-like modifier-activating enzyme 6

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