SMTL ID : 7zh9.1

Uba1 in complex with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: R.21, V.440, G.441, S.442, G.443, A.444, T.469, D.470, N.471, D.472, N.478, R.481, Q.482, K.494, D.518, K.519, V.520, A.542, L.543, D.544, N.545, A.548 Ligands: MG.4, MG.6 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:G.443, A:A.444, A:D.470, A:D.472, A:D.472, A:N.478, A:Q.482, A:K.494, A:V.520, A:V.520, A:N.545 Water bridges: A:R.21, A:I.445, A:I.445, A:R.481, A:R.481, A:R.481, A:D.544, A:D.544, A:A.548, A:A.548, A:I.863 Salt bridges: A:R.21, A:R.481, A:R.481, A:R.481, A:K.494, A:K.494

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: Y.24, V.25, L.26, G.27, D.175, G.178, K.381 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.178 Salt bridges: A:K.381

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 6 residues within 4Å: Chain A: L.114, D.115, V.117, D.136, K.139, I.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.114

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 2 residues within 4Å: Chain A: D.544 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.544, H2O.11, H2O.13 MG.5: 1 residues within 4Å: Chain A: E.231 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain A: D.472, E.475, N.478, K.494 Ligands: ATP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.472, H2O.2, H2O.3, H2O.7, H2O.11

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 11 residues within 4Å: Chain A: D.282, K.285, F.391, D.392, S.393, E.395, L.876, L.879, E.880, K.895, F.908 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.282, A:D.282, A:K.285, A:E.880 Water bridges: A:E.395 GOL.8: 12 residues within 4Å: Chain A: L.134, K.137, S.153, E.155, N.162, F.164, L.269, L.273, F.296, Q.297, H.300, F.388 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.153, A:E.155, A:N.162 Water bridges: A:Q.297, A:Y.390 GOL.9: 7 residues within 4Å: Chain A: P.176, G.208, N.209, F.210, V.258, K.259, V.260 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.208, A:N.209, A:V.260, A:V.260 Water bridges: A:G.208, A:F.210 GOL.10: 9 residues within 4Å: Chain A: K.33, R.150, F.171, T.172, L.174, A.377, C.378, S.379, G.380 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.150, A:T.172, A:T.172, A:T.172, A:C.378 Water bridges: A:R.150, A:T.172 GOL.11: 7 residues within 4Å: Chain A: G.567, T.568, L.569, K.572, G.573, N.574, F.898 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.568, A:N.574 Water bridges: A:N.574 GOL.12: 7 residues within 4Å: Chain A: L.737, Y.740, V.819, D.820, N.828, H.829, H.830 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.828, A:H.830 Water bridges: A:Y.740, A:Y.740, A:Y.740, A:D.820 GOL.13: 9 residues within 4Å: Chain A: A.499, E.500, C.503, L.509, K.510, G.511, K.512, I.513 Ligands: GOL.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.511, A:G.511, A:I.513 GOL.14: 5 residues within 4Å: Chain A: G.511, I.513, N.514, A.515 Ligands: GOL.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.511, A:I.513, A:N.514 GOL.15: 7 residues within 4Å: Chain A: T.183, G.184, M.185, I.254, N.607, K.608, R.713 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.607 Water bridges: A:K.608, A:R.713 GOL.16: 10 residues within 4Å: Chain A: E.16, S.17, S.20, R.21, K.476, S.477, K.823, D.824, D.826, K.856 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.477, A:D.824, A:K.856 Water bridges: A:D.826

1 x K: POTASSIUM ION(Non-covalent)

K.17: 5 residues within 4Å: Chain A: F.693, N.694, A.774, N.775, L.776 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.774, A:L.776, H2O.5

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

CL.18: 2 residues within 4Å: Chain A: I.847, E.848 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-activating enzyme E1 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ubiquitin-activating enzyme E1 1

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