SMTL ID : 6nya.2 (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 MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.537 Ligands: ATP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.537, H2O.6, H2O.8

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

ATP.2: 20 residues within 4Å: Chain A: R.14, G.434, G.436, A.437, D.463, N.464, 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.1 29 PLIP interactions: 27 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:D.537, A:N.538 Water bridges: A:R.14, A:R.14, A:R.14, A:R.14, A:I.438, A:R.474, A:R.474, A:R.474, A:R.474, A:D.537, 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

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

SO4.3: 4 residues within 4Å: Chain A: L.107, V.110, D.129, I.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.129 Water bridges: A:D.108, A:V.110 SO4.4: 7 residues within 4Å: Chain A: V.550, F.551, R.553, W.921, D.922, R.923, F.1012 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.553, A:W.921 Salt bridges: A:R.553, A:R.923 SO4.5: 4 residues within 4Å: Chain A: G.20, K.21, E.22 Ligands: EDO.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.21, A:E.22 Water bridges: A:K.374 Salt bridges: A:K.374 SO4.6: 6 residues within 4Å: Chain A: V.209, E.210, G.211, L.212, D.213, K.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.211, A:D.213, A:D.213 Salt bridges: A:K.243 SO4.7: 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 SO4.8: 3 residues within 4Å: Chain A: D.844, R.845, Q.846 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.845, A:Q.846 Salt bridges: A:R.845 SO4.9: 2 residues within 4Å: Chain A: R.298, K.317 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.298, A:K.317

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

EDO.10: 4 residues within 4Å: Chain A: N.538, V.539, D.540 Chain B: R.83 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.539, A:D.540, A:D.540, B:R.83, B:R.83 EDO.11: 7 residues within 4Å: Chain A: Y.17, V.18, L.19, G.20, G.171, K.374 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.171, A:K.374 Water bridges: A:L.16 EDO.12: 4 residues within 4Å: Chain A: I.7, D.8, E.9, S.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.7, A:E.9, A:S.10, A:S.10 EDO.13: 6 residues within 4Å: Chain A: E.6, I.7, D.8, Y.12, Q.28, Y.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.8 EDO.14: 4 residues within 4Å: Chain A: R.547, V.550, I.995, F.1012 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.547 EDO.15: 6 residues within 4Å: Chain A: N.31, S.55, T.57, N.102, Q.115, F.116 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.55, A:S.55, A:N.102, A:Q.115 Water bridges: A:T.57 EDO.16: 4 residues within 4Å: Chain A: R.143, F.164, T.165, G.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.143, A:T.165, A:T.165 EDO.17: 5 residues within 4Å: Chain A: E.148, F.289, Q.290, H.293, Y.383 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.289 Water bridges: A:K.130 EDO.18: 2 residues within 4Å: Chain A: R.305, E.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.305, A:R.305 Water bridges: A:N.308, A:N.308

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
D

B
E

C
F

Ubiquitin-activating enzyme E1 1

Ubiquitin

Ubiquitin-conjugating enzyme E2-34 kDa

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