SMTL ID : 7qs2.1

Crystal structure of B30.2 PRYSPRY domain of TRIM15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

4 x IOD: IODIDE ION(Non-functional Binders)

IOD.1: 2 residues within 4Å: Chain A: P.14, R.45 Ligand excluded by PLIP IOD.2: 3 residues within 4Å: Chain A: S.42, P.43 Ligands: EDO.13 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: K.170, K.171 Ligand excluded by PLIP IOD.4: 4 residues within 4Å: Chain A: D.68, Q.70, C.174, T.176 Ligand excluded by PLIP

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

EDO.5: 4 residues within 4Å: Chain A: G.8, F.58, H.63, R.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.64, A:R.64 EDO.6: 5 residues within 4Å: Chain A: T.33, R.34, Q.35, K.171 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.34, A:Q.35, A:K.171 EDO.7: 3 residues within 4Å: Chain A: R.34, Q.35 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) EDO.8: 6 residues within 4Å: Chain A: V.22, L.23, S.24, S.29, V.30, R.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.22, A:S.29 EDO.9: 3 residues within 4Å: Chain A: W.111, G.117, D.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.117 EDO.10: 4 residues within 4Å: Chain A: Q.70, L.71, H.107, R.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.71 Water bridges: A:L.69 EDO.11: 3 residues within 4Å: Chain A: D.73, G.74, H.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.74 EDO.12: 4 residues within 4Å: Chain A: G.83, G.85, V.86, D.98 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.85 EDO.13: 5 residues within 4Å: Chain A: D.41, S.42, D.47, K.89 Ligands: IOD.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.42, A:D.47, A:K.89 Water bridges: A:D.41, A:D.41 EDO.14: 7 residues within 4Å: Chain A: S.18, S.20, F.46, D.47, G.48, L.49, P.50 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.20, A:S.20, A:F.46, A:G.48 Water bridges: A:R.19 EDO.15: 5 residues within 4Å: Chain A: D.13, T.16, L.44, R.88, F.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.13, A:R.88, A:R.88 EDO.16: 1 residues within 4Å: Chain A: P.40 No protein-ligand interaction detected (PLIP) EDO.17: 1 residues within 4Å: Chain A: D.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.73

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

TRIM15: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

TRIM15