Research workbench
Mitochondrial ATPase protease YME1
Analyse Mitochondrial ATPase protease YME1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AZ0
- Type
- protein
- Length
- 2,644 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial inner membrane I-aaa protease supercomplex subunit YME1; POLY(UNK)
- UniProt
- B3LL85
- Ligands
- ATP, ADP, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Mitochondrial inner membrane I-aaa protease supercomplex subunit YME1 | protein | 439 | 51% helix, 10% strand | B3LL85 |
| G | POLY(UNK) | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · chains E
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.82 | 0.83 | 122 | ZN, ADP |
| 2 | 990 | 0.80 | 0.81 | 105 | ATP, MG |
| 3 | 1121 | 0.78 | 0.80 | 119 | ZN |
| 4 | 761 | 0.78 | 0.82 | 91 | ZN |
| 5 | 611 | 0.77 | 0.83 | 69 | ATP, MG |
Interfaces
13 interfaces between chains.
- D–E · 3164 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 3160 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 3064 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 3051 Ų buried · 24 hydrogen bonds · protein-protein
- A–F · 2280 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6AZ0 · Mitochondrial ATPase Protease YME1 · the same entry in another collection · chain A against A, TM-score 1.00
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 B3LL85
- Elsewhere: RCSB PDB 6AZ0 · PDBe 6AZ0 · UniProt B3LL85
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