SMTL ID : 6o83.1 (1 other biounit)

S. pombe ubiquitin E1~ubiquitin-AMP tetrahedral intermediate mimic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: H.294, E.309 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.294, A:E.309, A:E.309

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 6 residues within 4Å: Chain A: E.516, E.542, R.908, N.910, H.977, C.998 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.542, A:R.908, A:N.910, A:H.977

5 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 3 residues within 4Å: Chain A: T.164, Y.367, I.881 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.367 MPD.4: 5 residues within 4Å: Chain A: Q.125, A.141, S.150, F.284, Y.374 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.284, A:Y.374 MPD.5: 5 residues within 4Å: Chain A: E.647, K.648, E.654, M.657, L.661 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.654, A:E.654, A:L.661 MPD.6: 5 residues within 4Å: Chain A: R.536, V.539, V.979, E.981, F.996 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.536, A:V.539, A:V.979, A:E.981, A:F.996, A:F.996 Hydrogen bonds: A:R.536, A:E.981 MPD.7: 5 residues within 4Å: Chain A: I.705, H.706, F.711, P.733, E.737 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.733 Hydrogen bonds: A:E.737

1 x VMX: 5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine(Covalent)

VMX.8: 19 residues within 4Å: Chain A: G.423, G.425, A.426, I.427, D.452, M.453, D.454, K.476, E.500, R.501, V.502, A.524, L.525, D.526, N.527, A.530, T.550, C.582 Chain B: G.75 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.426, A:I.427, A:K.476, A:V.502, A:V.502, A:L.525, A:N.527

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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