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
- 4A5X
- Type
- protein
- Length
- 176 residues
- Chains
- 4
- 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
- Ligands
- P15
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mit domain-containing protein 1 | protein | 73 | 88% helix, 0% strand | Q8WV92 |
| B | Mit domain-containing protein 1 | protein | 73 | 88% helix, 0% strand | Q8WV92 |
| C | Charged multivesicular body protein 1A | protein | 14 | 86% helix, 0% strand | Q9HD42 |
| D | Charged multivesicular body protein 1A | protein | 16 | 75% helix, 0% strand | Q9HD42 |
Ligands and binding sites
- P15 · 2,5,8,11,14,17-hexaoxanonadecan-19-ol · ligand · chains B
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.54 | 0.89 | 22 | empty |
| 2 | 137 | 0.42 | 0.75 | 32 | empty |
Interfaces
5 interfaces between chains.
- B–D · 708 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 676 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 493 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 89 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 62 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4A5X · 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 B against A, TM-score 0.98
- Q9HD42 · AlphaFold monomer V2.0 prediction for charged multivesicular body protein 1A (Q9HD42) · a predicted model of the same protein · chain C against A, TM-score 0.88
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 4A5X · PDBe 4A5X · UniProt Q8WV92 · UniProt Q9HD42
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