Research workbench
Structures of MITD1
Analyse Structures of MITD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YMB
- Type
- protein
- Length
- 794 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mit domain-containing protein 1; Charged multivesicular body protein 1A
- UniProt
- Q8WV92, Q9HD42
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mit domain-containing protein 1 | protein | 153 | 24% helix, 25% strand | Q8WV92 |
| C | Mit domain-containing protein 1 | protein | 229 | 39% helix, 17% strand | Q8WV92 |
| D | Mit domain-containing protein 1 | protein | 231 | 40% helix, 16% strand | Q8WV92 |
| F, H | Charged multivesicular body protein 1A | protein | 14 | 71% helix, 0% strand | Q9HD42 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.78 | 0.93 | 26 | empty |
| 2 | 306 | 0.73 | 0.85 | 33 | empty |
| 3 | 234 | 0.53 | 0.76 | 26 | empty |
| 4 | 246 | 0.51 | 0.75 | 27 | empty |
| 5 | 102 | 0.35 | 0.74 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1335 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1295 Ų buried · 15 hydrogen bonds · protein-protein
- D–H · 707 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 700 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 91 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2YMB · Structures of MITD1 · the same entry in another collection · chain D against D, TM-score 1.00
- Q8WV92 · AlphaFold monomer V2.0 prediction for mit domain-containing protein 1 (Q8WV92) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9HD42 · AlphaFold monomer V2.0 prediction for charged multivesicular body protein 1A (Q9HD42) · a predicted model of the same protein · chain F against A, TM-score 0.63
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 Q8WV92
- Every structure of UniProt Q9HD42
- Elsewhere: RCSB PDB 2YMB · PDBe 2YMB · UniProt Q8WV92 · UniProt Q9HD42
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