MolNFT v1 · #163505 · protein
Crystal structure of TRIM21 ring domain in complex with an isopeptide- linked UBE2N~UBIQUITIN conjugate
6S53 · Ubiquitin-conjugating enzyme E2 N: “Crystal structure of TRIM21 ring domain in complex with an isopeptide- linked UBE2N~UBIQUITIN conjugate”. X-ray diffraction, 1 ligand (ZN), 16 pockets (best druggability 0.76). MolNFT v1 #163505…
- PDB
- 6S53
- Type
- protein
- Length
- 1,214 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 N; Polyubiquitin-C; E3 ubiquitin-protein ligase TRIM21
- EC
- 2.3.2.23, 2.3.2.27
- UniProt
- P61088, P0CG48, P19474
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 148 | 35% helix, 22% strand | P61088 |
| F, D, L, J | Polyubiquitin-C | protein | 76 | 20% helix, 33% strand | P0CG48 |
| C, K, I | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 149 | 35% helix, 22% strand | P61088 |
| B, A | E3 ubiquitin-protein ligase TRIM21 (EC 2.3.2.27) | protein | 79 | 42% helix, 20% strand | P19474 |
| H | E3 ubiquitin-protein ligase TRIM21 (EC 2.3.2.27) | protein | 76 | 42% helix, 18% strand | P19474 |
| G | E3 ubiquitin-protein ligase TRIM21 (EC 2.3.2.27) | protein | 81 | 44% helix, 17% strand | P19474 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains B, A, H, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.76 | 0.79 | 105 | empty |
| 2 | 80 | 0.76 | 0.98 | 19 | empty |
| 3 | 64 | 0.73 | 0.98 | 20 | empty |
| 4 | 68 | 0.72 | 0.97 | 21 | empty |
| 5 | 58 | 0.71 | 0.98 | 22 | empty |
Interfaces
25 interfaces between chains.
- B–A · 1187 Ų buried · 22 hydrogen bonds · protein-protein
- H–G · 1070 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 990 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 972 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 968 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 isopeptide (isopeptide).
Compared structures
- 6S53 · Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked… · the same entry in another collection · chain G against G, 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 P61088
- Every structure of UniProt P0CG48
- Every structure of UniProt P19474
- Elsewhere: RCSB PDB 6S53 · PDBe 6S53 · UniProt P61088 · UniProt P0CG48 · UniProt P19474
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