MolNFT v1 · #148763 · protein
Crystal structure of TRIM21 E3 ligase, ring domain in complex with its cognate E2 conjugating enzyme UBE2E1
6FGA · E3 ubiquitin-protein ligase TRIM21: “Crystal structure of TRIM21 E3 ligase, ring domain in complex with its cognate E2 conjugating enzyme UBE2E1”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 6FGA
- Type
- protein
- Length
- 1,667 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase TRIM21; Ubiquitin-conjugating enzyme E2 E1
- EC
- 2.3.2.27, 2.3.2.23, 2.3.2.24
- UniProt
- P19474, P51965
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 10 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase TRIM21 (EC 2.3.2.27) | protein | 76 | 36% helix, 16% strand | P19474 |
| B | E3 ubiquitin-protein ligase TRIM21 (EC 2.3.2.27) | protein | 76 | 38% helix, 16% strand | P19474 |
| C, E | E3 ubiquitin-protein ligase TRIM21 (EC 2.3.2.27) | protein | 79 | 39% helix, 15% strand | P19474 |
| D | E3 ubiquitin-protein ligase TRIM21 (EC 2.3.2.27) | protein | 71 | 34% helix, 17% strand | P19474 |
| F, G, H | E3 ubiquitin-protein ligase TRIM21 (EC 2.3.2.27) | protein | 77 | 43% helix, 17% strand | P19474 |
| I, M | Ubiquitin-conjugating enzyme E2 E1 (EC 2.3.2.23, 2.3.2.24) | protein | 150 | 38% helix, 18% strand | P51965 |
| J | Ubiquitin-conjugating enzyme E2 E1 (EC 2.3.2.23, 2.3.2.24) | protein | 156 | 40% helix, 17% strand | P51965 |
| K | Ubiquitin-conjugating enzyme E2 E1 (EC 2.3.2.23, 2.3.2.24) | protein | 151 | 38% helix, 18% strand | P51965 |
| L, O | Ubiquitin-conjugating enzyme E2 E1 (EC 2.3.2.23, 2.3.2.24) | protein | 148 | 37% helix, 18% strand | P51965 |
| N | Ubiquitin-conjugating enzyme E2 E1 (EC 2.3.2.23, 2.3.2.24) | protein | 152 | 39% helix, 18% strand | P51965 |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 4 copies · chains I, J, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.67 | 0.77 | 41 | empty |
| 2 | 525 | 0.64 | 0.76 | 39 | empty |
| 3 | 395 | 0.61 | 0.77 | 50 | empty |
| 4 | 179 | 0.56 | 0.80 | 23 | empty |
| 5 | 191 | 0.54 | 0.79 | 22 | empty |
Interfaces
22 interfaces between chains.
- A–E · 1234 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1218 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1204 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1076 Ų buried · 16 hydrogen bonds · protein-protein
- E–N · 518 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6FGA · Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2… · the same entry in another collection · chain K against K, TM-score 1.00
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 P19474
- Every structure of UniProt P51965
- Elsewhere: RCSB PDB 6FGA · PDBe 6FGA · UniProt P19474 · UniProt P51965
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