SMTL ID : 7qrz.1

Crystal structure of B30.2 PRYSPRY domain of MID2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.100, H.121 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.121 Water bridges: A:R.100, A:L.122, A:L.122 Salt bridges: A:R.100, A:H.121

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

EDO.2: 10 residues within 4Å: Chain A: S.4, Q.5, F.7, I.55, H.62, Y.63, W.64, S.173, G.174, L.175 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.5, A:H.62, A:G.174, A:L.175 EDO.3: 9 residues within 4Å: Chain A: A.52, F.56, A.79, Y.80, K.81, A.83, W.88, C.159 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.80 EDO.4: 6 residues within 4Å: Chain A: M.13, K.81, A.83, K.85, W.88 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.88 EDO.5: 5 residues within 4Å: Chain A: V.67, S.168, L.169, M.170 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.169 Water bridges: A:S.70 EDO.6: 3 residues within 4Å: Chain A: G.69, S.70 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.70, A:S.70 Water bridges: A:S.70 EDO.7: 2 residues within 4Å: Chain A: C.101, N.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.104 EDO.8: 5 residues within 4Å: Chain A: V.107, H.109, K.112, M.114, F.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.109, A:K.112 EDO.9: 4 residues within 4Å: Chain A: V.116, D.117, H.146, L.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.117, A:L.147 Water bridges: A:D.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhubi, R. et al., Structural analysis of TRIM family PRYSPRY domains and its implications for E3-ligand design. J Struct Biol X (2025)

Release Date

2022-05-04

Peptides

Probable E3 ubiquitin-protein ligase MID2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable E3 ubiquitin-protein ligase MID2

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