MolNFT v1 · #104959 · protein
Crystal structure of mitochondrial import inner membrane translocase subunit TIM50
4QQF: “Crystal structure of mitochondrial import inner membrane translocase subunit TIM50”. X-ray diffraction, 1 ligand (MG), 13 pockets (best druggability 0.88). MolNFT v1 #104959 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4QQF
- Type
- protein
- Length
- 1,132 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial import inner membrane translocase subunit TIM50
- UniProt
- Q02776
- Ligands
- MG
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Mitochondrial import inner membrane translocase subunit TIM50 | protein | 187 | 32% helix, 21% strand | Q02776 |
| A | Mitochondrial import inner membrane translocase subunit TIM50 | protein | 198 | 33% helix, 19% strand | Q02776 |
| B | Mitochondrial import inner membrane translocase subunit TIM50 | protein | 181 | 35% helix, 22% strand | Q02776 |
| C | Mitochondrial import inner membrane translocase subunit TIM50 | protein | 193 | 33% helix, 21% strand | Q02776 |
| E | Mitochondrial import inner membrane translocase subunit TIM50 | protein | 182 | 34% helix, 23% strand | Q02776 |
| F | Mitochondrial import inner membrane translocase subunit TIM50 | protein | 191 | 31% helix, 18% strand | Q02776 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains D, A, E, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.88 | 0.89 | 126 | MG |
| 2 | 592 | 0.83 | 0.88 | 91 | MG |
| 3 | 294 | 0.72 | 0.86 | 47 | empty |
| 4 | 139 | 0.64 | 0.86 | 24 | empty |
| 5 | 240 | 0.60 | 0.80 | 41 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1010 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 896 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 890 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 731 Ų buried · 1 hydrogen bond · protein-protein
- D–C · 706 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4QQF · Crystal structure of mitochondrial import inner membrane translocase subunit TIM50 · the same entry in another collection · chain F against F, TM-score 1.00
- Q02776 · AlphaFold monomer V2.0 prediction for mitochondrial import inner membrane translocase… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q02776
- Elsewhere: RCSB PDB 4QQF · PDBe 4QQF · UniProt Q02776
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