SMTL ID : 6cwy.1

Crystal structure of SUMO E1 in complex with an allosteric inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: H.162, L.287, P.288, F.291, Y.294 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.291 GOL.2: 8 residues within 4Å: Chain A: V.42, G.43, L.66, D.67, H.68, E.69, D.114, I.115 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.67, A:H.68, A:R.91, A:D.114, A:I.115

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain B: C.178, C.181, C.461, C.464 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.178, B:C.181, B:C.461, B:C.464

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain B: I.116, N.118, Y.121, H.144 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:I.116, B:Y.121, B:H.144

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

SO4.5: 6 residues within 4Å: Chain B: R.196, E.225, P.228, D.229, R.230, A.231 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.229, B:R.230, B:A.231 Salt bridges: B:R.196, B:R.230 SO4.6: 5 residues within 4Å: Chain B: R.139, P.185, T.186, R.188, S.398 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.186, B:T.186 Salt bridges: B:R.139, B:R.188 SO4.7: 3 residues within 4Å: Chain B: Q.94, K.97, A.111 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.97 SO4.8: 3 residues within 4Å: Chain B: F.437, N.439, V.450 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.439, B:N.439

1 x FHJ: dimethyl (1S,2S,3R,4R)-1-[(1S)-2-(4-methylphenyl)-1-(phenylamino)ethyl]-7-oxabicyclo[2.2.1]hept-5-ene-2,3-dicarboxylate(Covalent)

FHJ.9: 13 residues within 4Å: Chain A: Q.79, F.80, L.102 Chain B: C.50, E.51, L.53, K.54, V.57, L.58, A.96, S.99, V.100, F.103 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.80, A:L.102, B:K.54, B:K.54, B:V.57, B:L.58, B:V.100, B:V.100, B:F.103, B:F.103, B:F.103 pi-Stacking: A:F.80 Hydrogen bonds: B:C.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lv, Z. et al., Molecular mechanism of a covalent allosteric inhibitor of SUMO E1 activating enzyme. Nat Commun (2018)

Release Date

2019-01-16

Peptides

SUMO-activating enzyme subunit 1: A
SUMO-activating enzyme subunit 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

SUMO-activating enzyme subunit 1

SUMO-activating enzyme subunit 2

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