Research workbench
Human mitochondrial aaa protein ATAD1 (with a catalytic dead mutation) in complex with a peptide substrate (closed 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
- 7UPR
- Type
- protein
- Length
- 1,688 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, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 7 distinct chains · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Outer mitochondrial transmembrane helix translocase (EC 7.4.2.-) | protein | 298 | 47% helix, 9% strand | Q8NBU5 |
| B | Outer mitochondrial transmembrane helix translocase (EC 7.4.2.-) | protein | 277 | 49% helix, 9% strand | Q8NBU5 |
| E | Outer mitochondrial transmembrane helix translocase (EC 7.4.2.-) | protein | 300 | 45% helix, 9% strand | Q8NBU5 |
| D | Outer mitochondrial transmembrane helix translocase (EC 7.4.2.-) | protein | 299 | 46% helix, 9% strand | Q8NBU5 |
| F | Outer mitochondrial transmembrane helix translocase (EC 7.4.2.-) | protein | 269 | 39% helix, 6% strand | Q8NBU5 |
| A | Outer mitochondrial transmembrane helix translocase (EC 7.4.2.-) | protein | 235 | 46% helix, 9% strand | Q8NBU5 |
| G | Unknown peptide substrate | protein | 10 | 0% helix, 30% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains C, D, B, E, F
- MG · Magnesium ion · metal · 4 copies · chains C, D, B, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.84 | 0.85 | 102 | ATP, MG |
| 2 | 1077 | 0.82 | 0.83 | 88 | ATP, MG |
| 3 | 1200 | 0.82 | 0.83 | 101 | ATP, MG |
| 4 | 1171 | 0.80 | 0.81 | 128 | empty |
| 5 | 838 | 0.79 | 0.82 | 88 | ATP, MG |
Interfaces
11 interfaces between chains.
- E–D · 2259 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2254 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2207 Ų buried · 19 hydrogen bonds · protein-protein
- C–B · 2135 Ų buried · 10 hydrogen bonds · protein-protein
- F–A · 668 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7UPR · Human mitochondrial AAA protein ATAD1 (with a catalytic dead mutation) in complex with a… · the same entry in another collection · chain G against G, TM-score 1.00
- Q8NBU5 · AlphaFold monomer V2.0 prediction for outer mitochondrial transmembrane helix translocase… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 7UPR · PDBe 7UPR · UniProt Q8NBU5
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