SMTL ID : 6nya.1 (1 other biounit)

Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: R.14, G.434, G.436, A.437, D.463, D.465, N.471, R.474, Q.475, K.487, K.512, V.513, A.535, L.536, D.537, N.538, A.541 Chain B: G.85 Ligands: MG.2 26 PLIP interactions: 24 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:A.437, A:D.465, A:D.465, A:N.471, A:Q.475, A:K.487, A:V.513, A:V.513, A:N.538 Water bridges: A:R.14, A:I.438, A:R.474, A:R.474, A:R.474, A:D.817, A:I.856, A:I.856, A:I.856, B:G.85, B:G.85 Salt bridges: A:R.14, A:R.474, A:R.474, A:R.474, A:K.487, A:K.487

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.537 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.537, H2O.7, H2O.11

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

SO4.3: 4 residues within 4Å: Chain A: E.210, G.211, L.212, D.213 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.211, A:D.213, A:D.213, A:D.213 SO4.4: 3 residues within 4Å: Chain A: N.31, S.55, Q.115 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.55, A:S.55, A:Q.115 Water bridges: A:T.57 SO4.5: 1 residues within 4Å: Chain A: Q.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.117 SO4.6: 5 residues within 4Å: Chain A: R.547, V.550, F.551, I.995, F.1012 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.547 Water bridges: A:E.997 SO4.7: 3 residues within 4Å: Chain A: Y.458, V.460, N.507 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.507 SO4.8: 3 residues within 4Å: Chain A: D.844, R.845, Q.846 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.844, A:R.845, A:Q.846 Salt bridges: A:R.845 SO4.9: 3 residues within 4Å: Chain A: G.20, K.21, E.22 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.21, A:E.22 Water bridges: A:A.23, A:K.374 Salt bridges: A:K.21 SO4.10: 2 residues within 4Å: Chain A: R.281, N.337 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.337 Salt bridges: A:R.281

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

EDO.11: 4 residues within 4Å: Chain A: N.538, V.539, D.540 Chain B: R.83 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.539, A:D.540, A:D.540, B:R.83 Water bridges: A:R.854 EDO.12: 2 residues within 4Å: Chain A: R.89, A.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.89 Water bridges: A:R.89 EDO.13: 8 residues within 4Å: Chain A: D.275, K.278, F.384, D.385, S.386, E.388, K.888, F.901 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.275, A:D.275, A:K.278, A:S.386 Water bridges: A:D.385 EDO.14: 7 residues within 4Å: Chain A: E.208, I.247, N.600, R.706, F.839, I.840, E.841 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.600, A:E.841 EDO.15: 3 residues within 4Å: Chain A: S.139, S.140, G.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.140 EDO.16: 4 residues within 4Å: Chain A: E.527, F.551, Y.552, H.1016 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.527 Water bridges: A:R.553, A:R.923, A:D.925 EDO.17: 7 residues within 4Å: Chain A: L.127, E.148, N.155, F.289, Q.290, H.293, Y.383 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.155 Water bridges: A:K.130, A:N.155 EDO.18: 6 residues within 4Å: Chain A: E.6, I.7, D.8, Y.12, Q.28, Y.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.8, A:Q.28 Water bridges: A:Y.12 EDO.19: 5 residues within 4Å: Chain A: Y.912, Y.917, R.923, F.924, P.1011 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.912, A:R.923 EDO.20: 4 residues within 4Å: Chain A: F.814, E.815, K.816, G.853 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.814, A:K.816, A:K.816 Water bridges: A:K.816, A:G.853 EDO.21: 3 residues within 4Å: Chain A: N.427, G.454, S.455 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.427, A:S.455 EDO.22: 5 residues within 4Å: Chain C: Q.78, F.79, R.95, L.96, L.101 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.79, C:L.96, C:L.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, K.M. et al., Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34. Nat Commun (2019)

Release Date

2019-08-07

Peptides

Ubiquitin-activating enzyme E1 1: A
Ubiquitin: B
Ubiquitin-conjugating enzyme E2-34 kDa: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ubiquitin-activating enzyme E1 1

Ubiquitin

Ubiquitin-conjugating enzyme E2-34 kDa

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