SMTL ID : 8r5d.1

Crystal structure of human TRIM7 PRYSPRY domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

3 x MLA: MALONIC ACID(Non-covalent)

MLA.1: 6 residues within 4Å: Chain A: N.47, T.48, R.49, F.90, S.163, C.165 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.48, A:T.48, A:S.163, A:S.163 Salt bridges: A:R.49 MLA.8: 7 residues within 4Å: Chain B: N.47, T.48, R.49, F.90, S.163, C.165 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.48, B:S.163 Salt bridges: B:R.49 MLA.9: 9 residues within 4Å: Chain A: I.20, R.29 Chain B: S.22, G.27, R.29, Y.170, R.172 Ligands: EDO.15, EDO.16 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.170 Salt bridges: B:R.29, B:R.29, B:R.172, B:R.172

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

EDO.2: 3 residues within 4Å: Chain A: G.31, E.32, R.33 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.32, A:R.33, A:R.33 EDO.3: 7 residues within 4Å: Chain A: R.79, W.97, V.152, N.153, F.154, Q.155, E.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.155, A:E.156, A:E.156 EDO.4: 5 residues within 4Å: Chain A: S.69, L.101, G.104, Y.106, H.121 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.69 EDO.5: 3 residues within 4Å: Chain A: R.29, Y.170 Chain B: G.168 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.168 EDO.6: 7 residues within 4Å: Chain A: S.22, G.27, R.29, Y.170, R.172 Chain B: I.20 Ligands: EDO.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.29, A:R.29, A:R.172, A:R.172 EDO.7: 6 residues within 4Å: Chain A: T.14, C.42, L.51, E.80, R.84, F.159 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.80, A:E.80, A:R.84, A:R.84 EDO.10: 5 residues within 4Å: Chain B: T.14, L.51, E.80, R.84, F.159 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.80, B:R.84, B:R.84 EDO.11: 5 residues within 4Å: Chain A: R.172 Chain B: I.20, G.31, E.32, R.33 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.32, B:R.33, B:R.33, B:R.33, A:R.172 EDO.12: 6 residues within 4Å: Chain B: R.79, W.97, N.153, F.154, Q.155, E.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.155, B:E.156 EDO.13: 6 residues within 4Å: Chain B: N.47, L.87, T.88, P.89, F.90 Ligands: MLA.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.90 EDO.14: 5 residues within 4Å: Chain B: S.69, L.101, G.104, Y.106, H.121 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.69, B:Y.106, B:H.121 EDO.15: 3 residues within 4Å: Chain A: G.168 Chain B: Y.170 Ligands: MLA.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.29, A:R.29 Hydrogen bonds: B:R.29 EDO.16: 10 residues within 4Å: Chain A: I.20, L.21, S.22 Chain B: I.20, L.21, S.22, V.28, R.29 Ligands: EDO.6, MLA.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.20, B:R.29 EDO.17: 5 residues within 4Å: Chain B: N.16, R.18, D.45, T.46, T.48 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.16, B:N.16, B:R.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Munoz Sosa, C.J. et al., A C-Degron Structure-Based Approach for the Development of Ligands Targeting the E3 Ligase TRIM7. Acs Chem.Biol. (2024)

Release Date

2024-01-17

Peptides

E3 ubiquitin-protein ligase TRIM7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E3 ubiquitin-protein ligase TRIM7

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