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

HOIP-fragment5 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x FHH: methyl 4-[(2-oxidanylidene-1,5,6,7-tetrahydrocyclopenta[b]pyridin-3-yl)carbonylamino]butanoate(Covalent)

FHH.1: 12 residues within 4Å: Chain A: I.20, Y.29, L.31, A.32, R.33, C.36, H.38, F.39, H.40, T.42, S.50, Q.125 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.29, A:L.31, A:F.39 Hydrogen bonds: A:H.38, A:H.40, A:H.40, A:S.50 Water bridges: A:H.38 pi-Stacking: A:F.39

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: C.22, K.24, C.25, C.41, Q.43, C.44, H.46 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.22, A:C.25, A:C.41, A:C.44 ZN.3: 6 residues within 4Å: Chain A: C.49, C.52, H.77, P.78, C.81, F.83 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.49, A:C.52, A:H.77, A:C.81 ZN.4: 5 residues within 4Å: Chain A: C.62, E.64, C.67, H.74, H.76 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.62, A:C.67, A:H.74, A:H.76 ZN.5: 6 residues within 4Å: Chain A: C.120, V.122, C.137, K.139, C.149, H.152 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.120, A:C.137, A:C.149, A:H.152

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

SO4.6: 7 residues within 4Å: Chain A: N.54, P.78, L.214, G.215, Q.216, S.217 Ligands: NA.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.54, A:Q.216, A:S.217, A:S.217 SO4.7: 6 residues within 4Å: Chain A: T.89, A.90, L.91, Y.145, Q.150, K.154 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.90, A:Y.145, A:Q.150 Salt bridges: A:K.154 SO4.8: 3 residues within 4Å: Chain A: Y.14, R.221, R.222 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.222 Water bridges: A:R.222 Salt bridges: A:R.221, A:R.222

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

EDO.9: 8 residues within 4Å: Chain A: R.79, Y.84, Y.172, E.176, T.179, A.180, R.183, Y.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.183, A:Y.184 EDO.10: 11 residues within 4Å: Chain A: N.18, R.33, G.51, L.82, V.158, S.159, N.162, I.218, P.219, R.220, R.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.18, A:N.18, A:N.162

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 3 residues within 4Å: Chain A: H.76, Y.184 Ligands: SO4.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, H. et al., Fragment-Based Covalent Ligand Screening Enables Rapid Discovery of Inhibitors for the RBR E3 Ubiquitin Ligase HOIP. J. Am. Chem. Soc. (2019)

Release Date

2019-01-30

Peptides

E3 ubiquitin-protein ligase RNF31: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E3 ubiquitin-protein ligase RNF31

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