Research workbench
Crystal structure of TRIM33 phd-bromo in the free state
Analyse Crystal structure of TRIM33 phd-bromo in the free state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U5M
- Type
- protein
- Length
- 2,114 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase TRIM33
- EC
- 6.3.2.-
- UniProt
- Q9UPN9
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 12 distinct chains · 41% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 178 | 42% helix, 2% strand | Q9UPN9 |
| B | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 178 | 40% helix, 2% strand | Q9UPN9 |
| C | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 174 | 41% helix, 3% strand | Q9UPN9 |
| D | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 177 | 41% helix, 3% strand | Q9UPN9 |
| E | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 173 | 43% helix, 3% strand | Q9UPN9 |
| F | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 179 | 41% helix, 2% strand | Q9UPN9 |
| G | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 180 | 41% helix, 3% strand | Q9UPN9 |
| H | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 178 | 39% helix, 3% strand | Q9UPN9 |
| I | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 173 | 40% helix, 2% strand | Q9UPN9 |
| J | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 174 | 42% helix, 3% strand | Q9UPN9 |
| K | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 175 | 41% helix, 3% strand | Q9UPN9 |
| L | E3 ubiquitin-protein ligase TRIM33 (EC 6.3.2.-) | protein | 175 | 43% helix, 3% strand | Q9UPN9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.72 | 0.76 | 93 | empty |
| 2 | 887 | 0.70 | 0.75 | 77 | empty |
| 3 | 865 | 0.70 | 0.75 | 90 | empty |
| 4 | 731 | 0.65 | 0.74 | 66 | empty |
| 5 | 646 | 0.63 | 0.74 | 58 | empty |
Interfaces
23 interfaces between chains.
- H–K · 416 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 415 Ų buried · 12 hydrogen bonds · protein-protein
- I–K · 409 Ų buried · 8 hydrogen bonds · protein-protein
- C–H · 404 Ų buried · 7 hydrogen bonds · protein-protein
- B–J · 400 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3U5M · Crystal structure of TRIM33 PHD-Bromo in the free state · the same entry in another collection · chain L against L, 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 Q9UPN9
- Elsewhere: RCSB PDB 3U5M · PDBe 3U5M · UniProt Q9UPN9
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