SMTL ID : 6o82.2 (1 other biounit)

S. pombe ubiquitin E1 complex with a ubiquitin-AMP mimic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.526 Ligands: POP.3, JZU.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.526, H2O.1, H2O.1 MG.2: 4 residues within 4Å: Chain A: D.454, E.457, N.460 Ligands: POP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.454

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.3: 10 residues within 4Å: Chain A: R.11, D.454, N.460, R.463, Q.464, K.476, D.526 Ligands: MG.1, MG.2, JZU.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.460, A:Q.464 Water bridges: A:R.463 Salt bridges: A:R.11, A:R.463, A:R.463, A:K.476

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

SO4.4: 3 residues within 4Å: Chain A: P.504, Y.533, R.536 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.536 SO4.5: 5 residues within 4Å: Chain A: E.507, F.974, R.975, K.976, H.977 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.974, A:K.976, A:H.977 Salt bridges: A:R.975, A:H.977

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

EDO.6: 3 residues within 4Å: Chain A: G.17, H.18, F.831 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.18

1 x JZU: 5'-deoxy-5'-(sulfamoylamino)adenosine(Covalent)

JZU.7: 20 residues within 4Å: Chain A: G.423, G.425, A.426, D.452, M.453, D.454, 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.76 Ligands: MG.1, POP.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.426, A:D.454, A:R.463, A:Q.464, A:K.476, A:V.502, A:V.502, A:N.527 Water bridges: A:G.425, A:A.524

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hann, Z.S. et al., Structural basis for adenylation and thioester bond formation in the ubiquitin E1. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-06-19

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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