MolNFT v1 · #85228 · protein
Structures of MITD1
4A5Z · Mit domain-containing protein 1: “Structures of MITD1”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.76). MolNFT v1 #85228 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4A5Z
- Type
- protein
- Length
- 624 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mit domain-containing protein 1
- UniProt
- Q8WV92
- Ligands
- CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Mit domain-containing protein 1 | protein | 155 | 28% helix, 27% strand | Q8WV92 |
| B, D | Mit domain-containing protein 1 | protein | 157 | 28% helix, 27% strand | Q8WV92 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.76 | 0.86 | 36 | CL |
| 2 | 332 | 0.75 | 0.86 | 30 | CL |
| 3 | 297 | 0.57 | 0.77 | 29 | CL |
| 4 | 229 | 0.54 | 0.77 | 31 | CL |
| 5 | 175 | 0.49 | 0.77 | 30 | CL |
Interfaces
3 interfaces between chains.
- B–D · 1390 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1376 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
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
- Elsewhere: RCSB PDB 4A5Z · PDBe 4A5Z · UniProt Q8WV92
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