SMTL ID : 6o82.1 (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.11 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.526, H2O.3, H2O.4 MG.2: 4 residues within 4Å: Chain A: D.454, N.460, K.476 Ligands: POP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.454, H2O.1, H2O.1, H2O.2, H2O.2

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

POP.3: 11 residues within 4Å: Chain A: R.11, D.454, N.460, R.463, Q.464, K.476, D.526, K.801 Ligands: MG.1, MG.2, JZU.11 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.460, A:N.460, A:Q.464, A:D.526 Water bridges: A:N.460, A:R.463, A:R.463, A:D.526, A:V.841, A:V.841 Salt bridges: A:R.11, A:R.463, A:R.463, A:K.476, A:K.801 POP.4: 3 residues within 4Å: Chain A: G.17, H.18, E.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.18, A:E.19 Salt bridges: A:H.18

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

SO4.5: 3 residues within 4Å: Chain A: R.975, H.977, V.979 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.979 Water bridges: A:R.537, A:R.975 Salt bridges: A:R.975, A:H.977 SO4.6: 5 residues within 4Å: Chain A: H.133, H.136, G.156, E.157, N.158 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.157, A:N.158, A:N.158 Salt bridges: A:H.136 SO4.7: 4 residues within 4Å: Chain A: T.3, I.4, E.6, H.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.3, A:I.4, A:E.6 Salt bridges: A:H.18 SO4.8: 5 residues within 4Å: Chain A: N.28, S.52, T.54, N.111, F.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.52, A:T.54 Water bridges: A:N.28 SO4.9: 5 residues within 4Å: Chain A: V.204, K.205, G.206, M.207, P.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.206, A:M.207 Salt bridges: A:K.205

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

EDO.10: 3 residues within 4Å: Chain A: D.829, R.830, F.831 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.830, A:F.831

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

JZU.11: 22 residues within 4Å: Chain A: V.422, 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.75, G.76 Ligands: MG.1, POP.3 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.426, A:R.463, A:Q.464, A:K.476, A:V.502, A:V.502, A:L.525, A:D.526, A:N.527, B:G.76 Water bridges: A:I.427, B:G.76, B:G.76

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
A

B
B

Ubiquitin-activating enzyme E1 1

Ubiquitin-60S ribosomal protein L40

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