SMTL ID : 6o83.2 (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.542, R.908, N.910, H.977, C.998, K.1000 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.542, A:E.542, A:R.908, A:N.910, A:K.1000, A:K.1000

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

MPD.3: 6 residues within 4Å: Chain A: E.647, K.648, P.649, E.654, L.661, Y.743 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.661, A:Y.743 MPD.4: 6 residues within 4Å: Chain A: I.32, D.57, P.58, Q.59, E.119, T.120 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.59 Hydrogen bonds: A:D.57, A:E.119 MPD.5: 3 residues within 4Å: Chain A: E.566, S.571 Chain B: Q.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.566, A:S.571 MPD.6: 3 residues within 4Å: Chain A: I.705, F.711, E.737 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.705, A:F.711 Hydrogen bonds: A:E.737 MPD.7: 7 residues within 4Å: Chain A: L.122, Q.125, A.141, S.150, F.284, Q.285, Y.374 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.122, A:A.141, A:F.284 Hydrogen bonds: A:Y.374, A:Y.374 MPD.8: 4 residues within 4Å: Chain A: V.539, V.979, E.981, F.996 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.979, A:E.981, A:F.996, A:F.996 Hydrogen bonds: A:E.981

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

VMX.9: 19 residues within 4Å: Chain A: G.423, G.425, A.426, I.427, T.451, D.452, M.453, D.454, K.476, R.501, V.502, A.524, L.525, D.526, N.527, T.550, C.582 Chain B: R.74, 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
C

B
D

Ubiquitin-activating enzyme E1 1

Ubiquitin-60S ribosomal protein L40

Related Entries With Identical Sequence