SMTL ID : 4ii3.2 (1 other biounit)

Crystal structure of S. pombe Ubiquitin activating enzyme 1 (Uba1) in complex with ubiquitin and ATP/Mg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.526 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: D.454, E.457 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.457

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

ATP.3: 22 residues within 4Å: Chain A: R.11, G.423, G.425, A.426, D.452, M.453, D.454, N.460, R.463, Q.464, K.476, R.501, V.502, A.524, L.525, D.526, N.527, A.530, K.801 Chain B: G.96 Ligands: MG.1, MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.426, A:D.454, A:N.460, A:Q.464, A:K.476, A:V.502, A:V.502, A:D.526, A:N.527 Salt bridges: A:R.11, A:R.463, A:R.463, A:K.476, A:K.476, A:K.801

6 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: D.985, G.989 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.985, H2O.2 CA.5: 1 residues within 4Å: Chain A: D.907 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: D.600, Q.608 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: Y.909, E.927 No protein-ligand interaction detected (PLIP) CA.8: 2 residues within 4Å: Chain A: K.900, Y.909 No protein-ligand interaction detected (PLIP) CA.9: 1 residues within 4Å: Chain A: T.646 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.646

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Ubiquitin-activating enzyme E1 1

Ubiquitin-60S ribosomal protein L40

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