Research workbench
Crystal structure of nhl domain of TRIM2 (full C-terminal)
Analyse Crystal structure of nhl domain of TRIM2 (full C-terminal) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QRV
- Type
- protein
- Length
- 1,113 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tripartite motif-containing protein 2
- EC
- 2.3.2.27
- UniProt
- Q9C040
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tripartite motif-containing protein 2 (EC 2.3.2.27) | protein | 278 | 2% helix, 49% strand | Q9C040 |
| B | Tripartite motif-containing protein 2 (EC 2.3.2.27) | protein | 276 | 2% helix, 49% strand | Q9C040 |
| D | Tripartite motif-containing protein 2 (EC 2.3.2.27) | protein | 281 | 2% helix, 48% strand | Q9C040 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 26 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.82 | 0.83 | 73 | EDO |
| 2 | 964 | 0.80 | 0.81 | 68 | EDO |
| 3 | 382 | 0.67 | 0.80 | 46 | EDO |
| 4 | 350 | 0.66 | 0.80 | 37 | EDO |
| 5 | 346 | 0.65 | 0.80 | 36 | EDO |
Interfaces
4 interfaces between chains.
- A–D · 719 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 667 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 240 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 141 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7QRV · Crystal structure of NHL domain of TRIM2 (full C-terminal) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9C040 · AlphaFold monomer V2.0 prediction for tripartite motif-containing protein 2 (Q9C040) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9C040
- Elsewhere: RCSB PDB 7QRV · PDBe 7QRV · UniProt Q9C040
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