Research workbench
Crystal structure of TRIM21 E3 ligase, ring domain in complex with its cognate E2 conjugating enzyme UBE2E1
Analyse Crystal structure of TRIM21 E3 ligase, ring domain in complex with its cognate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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