Research workbench
Human mitochondrial aaa protein ATAD1 (with a catalytic dead mutation) in complex with a peptide substrate (open conformation)
Analyse Human mitochondrial aaa protein ATAD1 (with a catalytic dead mutation) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UPT
- Type
- protein
- Length
- 1,702 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer mitochondrial transmembrane helix translocase; Unknown peptide substrate
- EC
- 7.4.2.-
- UniProt
- Q8NBU5
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer mitochondrial transmembrane helix translocase (EC 7.4.2.-) | protein | 273 | 47% helix, 7% strand | Q8NBU5 |
| B | Outer mitochondrial transmembrane helix translocase (EC 7.4.2.-) | protein | 297 | 48% helix, 9% strand | Q8NBU5 |
| C | Outer mitochondrial transmembrane helix translocase (EC 7.4.2.-) | protein | 299 | 49% helix, 8% strand | Q8NBU5 |
| D | Outer mitochondrial transmembrane helix translocase (EC 7.4.2.-) | protein | 294 | 48% helix, 7% strand | Q8NBU5 |
| E | Outer mitochondrial transmembrane helix translocase (EC 7.4.2.-) | protein | 293 | 48% helix, 9% strand | Q8NBU5 |
| F | Outer mitochondrial transmembrane helix translocase (EC 7.4.2.-) | protein | 236 | 49% helix, 7% strand | Q8NBU5 |
| G | Unknown peptide substrate | protein | 10 | 0% helix, 10% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains B, D, C, A, E, F
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 5 copies · chains B, D, C, A, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.83 | 0.84 | 104 | ATP, MG |
| 2 | 1172 | 0.81 | 0.82 | 104 | MG, ATP |
| 3 | 649 | 0.81 | 0.86 | 54 | MG, ATP |
| 4 | 532 | 0.80 | 0.87 | 53 | ATP, MG |
| 5 | 690 | 0.80 | 0.84 | 58 | MG, ATP |
Interfaces
13 interfaces between chains.
- C–E · 2279 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 2275 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 2250 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 2192 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1969 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7UPT · Human mitochondrial AAA protein ATAD1 (with a catalytic dead mutation) in complex with a… · the same entry in another collection · chain E against E, TM-score 1.00
- Q8NBU5 · AlphaFold monomer V2.0 prediction for outer mitochondrial transmembrane helix translocase… · a predicted model of the same protein · chain A 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 Q8NBU5
- Elsewhere: RCSB PDB 7UPT · PDBe 7UPT · UniProt Q8NBU5
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