MolNFT v1 · #118858 · protein
Complex of TRIM25 ring with UBCH5-ub
5FER · E3 UBIQUITIN/ISG15 ligase TRIM25: “Complex of TRIM25 ring with UBCH5-ub”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.70). MolNFT v1 #118858 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FER
- Type
- protein
- Length
- 602 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 UBIQUITIN/ISG15 ligase TRIM25; Ubiquitin-conjugating enzyme E2 D1; Ubiquitin-40S…
- EC
- 6.3.2.-, 2.3.2.27, 2.3.2.23, 2.3.2.24
- UniProt
- Q14258, P51668, P62992
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 UBIQUITIN/ISG15 ligase TRIM25 (EC 6.3.2.-, 2.3.2.27) | protein | 79 | 33% helix, 16% strand | Q14258 |
| B | Ubiquitin-conjugating enzyme E2 D1 (EC 2.3.2.23, 2.3.2.24) | protein | 145 | 36% helix, 19% strand | P51668 |
| C, F | Ubiquitin-40S ribosomal protein S27A | protein | 76 | 24% helix, 34% strand | P62992 |
| D | E3 UBIQUITIN/ISG15 ligase TRIM25 (EC 6.3.2.-, 2.3.2.27) | protein | 80 | 38% helix, 16% strand | Q14258 |
| E | Ubiquitin-conjugating enzyme E2 D1 (EC 2.3.2.23, 2.3.2.24) | protein | 146 | 36% helix, 19% strand | P51668 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.70 | 0.87 | 43 | empty |
| 2 | 333 | 0.64 | 0.80 | 41 | empty |
| 3 | 68 | 0.44 | 0.82 | 21 | empty |
| 4 | 88 | 0.38 | 0.77 | 17 | empty |
| 5 | 89 | 0.35 | 0.75 | 18 | empty |
Interfaces
9 interfaces between chains.
- A–D · 1051 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 921 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 917 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 591 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 537 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5FER · Complex of TRIM25 RING with UbcH5-Ub · the same entry in another collection · chain F against F, TM-score 1.00
- P51668 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D1 (P51668) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q14258 · AlphaFold monomer V2.0 prediction for E3 UBIQUITIN/ISG15 ligase TRIM25 (Q14258) · a predicted model of the same protein · chain D against A, TM-score 0.96
- P62992 · AlphaFold monomer V2.0 prediction for ubiquitin-40S ribosomal protein S27A (P62992) · a predicted model of the same protein · chain C against A, TM-score 0.92
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q14258
- Every structure of UniProt P51668
- Every structure of UniProt P62992
- Elsewhere: RCSB PDB 5FER · PDBe 5FER · UniProt Q14258 · UniProt P51668 · UniProt P62992
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