MolNFT v1 · #173802 · protein
Crystal structure of monoubiquitinated TRIM21 ring (ub-ring) in complex with ubiquitin charged UBE2N (UBE2N~UB) and UBE2V2
7BBD · Polyubiquitin-B,E3 ubiquitin-protein ligase TRIM21: “Crystal structure of monoubiquitinated TRIM21 ring (ub-ring) in complex with ubiquitin charged UBE2N…”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.68).…
- PDB
- 7BBD
- Type
- protein
- Length
- 538 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-B,E3 ubiquitin-protein ligase TRIM21; Polyubiquitin-C…
- EC
- 2.3.2.27, 2.3.2.23
- UniProt
- J3QS39, P19474, P0CG48, Q15819, P61088
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Polyubiquitin-B,E3 ubiquitin-protein ligase TRIM21 (EC 2.3.2.27) | protein | 160 | 31% helix, 28% strand | J3QS39, P19474 |
| D | Polyubiquitin-C | protein | 76 | 20% helix, 36% strand | P0CG48 |
| A | Ubiquitin-conjugating enzyme E2 variant 2 | protein | 149 | 21% helix, 18% strand | Q15819 |
| C | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 153 | 34% helix, 21% strand | P61088 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.68 | 0.79 | 50 | empty |
| 2 | 139 | 0.60 | 0.84 | 20 | empty |
| 3 | 211 | 0.56 | 0.79 | 32 | empty |
| 4 | 156 | 0.47 | 0.76 | 22 | empty |
| 5 | 57 | 0.32 | 0.77 | 21 | empty |
Interfaces
4 interfaces between chains.
- D–C · 947 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 867 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 862 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 485 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 7BBD · Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin… · the same entry in another collection · chain B against B, TM-score 1.00
- Q15819 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 variant 2 (Q15819) · a predicted model of the same protein · chain A against A, TM-score 0.93
- P19474 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase TRIM21 (P19474) · a predicted model of the same protein · chain B against A, TM-score 0.50
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 J3QS39
- Every structure of UniProt P19474
- Every structure of UniProt P0CG48
- Every structure of UniProt Q15819
- Every structure of UniProt P61088
- Elsewhere: RCSB PDB 7BBD · PDBe 7BBD · UniProt J3QS39 · UniProt P19474 · UniProt P0CG48 · UniProt Q15819 · UniProt P61088
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