SMTL ID : 4ii2.1

Crystal structure of Ubiquitin activating enzyme 1 (Uba1) in complex with the Ub E2 Ubc4, ubiquitin, and ATP/Mg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.526 Ligands: ATP.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.526, H2O.1, H2O.1 MG.2: 3 residues within 4Å: Chain A: D.454, E.457 Ligands: ATP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.454, H2O.1, H2O.1, H2O.1, H2O.1

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

ATP.3: 24 residues within 4Å: Chain A: R.11, V.422, G.423, G.425, A.426, T.451, D.452, M.453, D.454, N.460, R.463, Q.464, K.476, E.500, R.501, V.502, A.524, L.525, D.526, N.527, A.530 Chain B: G.83 Ligands: MG.1, MG.2 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.426, A:D.454, A:D.454, A:D.454, A:N.460, A:Q.464, A:K.476, A:V.502, A:V.502, A:N.527 Water bridges: A:R.11, A:G.425, A:D.454, A:R.463, A:R.463, A:R.463, A:R.501, A:R.501, B:G.83, B:G.83, B:G.83 Salt bridges: A:R.11, A:R.463, A:R.463, A:R.463, A:K.476, A:K.476

1 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.4: 9 residues within 4Å: Chain A: D.270, K.273, F.375, D.376, S.377, E.379, L.854, L.857, F.886 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.270 Water bridges: A:D.376, A:L.854, A:E.858, A:K.861

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 7 residues within 4Å: Chain A: H.294, S.297, L.298, R.300, D.306, R.340 Ligands: SO4.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.297, A:S.297, A:D.306, A:R.340 EDO.6: 5 residues within 4Å: Chain A: T.3, I.4, D.5, Y.9, Y.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.5 Water bridges: A:Y.9 EDO.7: 5 residues within 4Å: Chain A: R.536, V.539, F.540, F.996 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.536 EDO.8: 5 residues within 4Å: Chain A: R.536, R.537, F.540, V.979 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.537 EDO.9: 7 residues within 4Å: Chain A: K.35, G.36, L.37, E.119, S.144, R.145, D.342 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.35, A:L.37, A:R.145, A:S.347 Water bridges: A:K.35, A:S.144, A:S.144, A:R.145, A:R.145, A:G.341 EDO.10: 6 residues within 4Å: Chain A: S.52, T.54, S.99, Y.108, N.111, F.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.99, A:S.99, A:N.111 Water bridges: A:T.54 EDO.14: 7 residues within 4Å: Chain A: Q.558, E.566, N.874, F.876, I.890 Chain B: R.49, Q.56 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.566, A:E.566, B:R.49, B:Q.56 Water bridges: A:Q.558, A:S.571, A:S.571, A:N.874, A:N.874, A:I.890

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

SO4.11: 3 residues within 4Å: Chain A: G.17, H.18, E.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.18, A:E.19 Water bridges: A:L.16, A:A.20, A:K.365 SO4.12: 4 residues within 4Å: Chain A: S.297, R.300, R.340 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.297 Salt bridges: A:R.340 SO4.13: 4 residues within 4Å: Chain A: R.634, L.776 Chain C: R.72, Y.145 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Salt bridges: A:R.634, C:R.72 Hydrogen bonds: C:Y.145, C:Y.145 SO4.15: 2 residues within 4Å: Chain B: R.36, R.40 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.36, B:R.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Olsen, S.K. et al., Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer. Mol.Cell (2013)

Release Date

2013-02-13

Peptides

Ubiquitin-activating enzyme E1 1: A
Ubiquitin-60S ribosomal protein L40: B
Ubiquitin-conjugating enzyme E2 4: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ubiquitin-activating enzyme E1 1

Ubiquitin-60S ribosomal protein L40

Ubiquitin-conjugating enzyme E2 4

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