Research workbench
S. cerevisiae ATM1 in MSP1D1 nanodiscs with bound AMP-pnp and MG2+
Analyse S. cerevisiae ATM1 in MSP1D1 nanodiscs with bound AMP-pnp and MG2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PSM
- Type
- protein
- Length
- 1,170 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-sulfur clusters transporter ATM1, mitochondrial
- EC
- 7.-.-.-
- UniProt
- P40416
- Ligands
- ANP, LOP, MG
- Pockets
- 14 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 61% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Iron-sulfur clusters transporter ATM1, mitochondrial (EC 7.-.-.-) | protein | 585 | 61% helix, 7% strand | P40416 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- LOP · (1R)-2-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(dodecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.87 | 0.88 | 113 | empty |
| 2 | 223 | 0.80 | 0.94 | 28 | empty |
| 3 | 513 | 0.79 | 0.86 | 69 | ANP, MG |
| 4 | 115 | 0.79 | 0.98 | 23 | empty |
| 5 | 475 | 0.78 | 0.86 | 64 | ANP, MG |
Interfaces
1 interface between chains.
- A–B · 8796 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 7PSM · S. cerevisiae Atm1 in MSP1D1 nanodiscs with bound AMP-PNP and Mg2+ · the same entry in another collection · chain A against A, TM-score 1.00
- P40416 · AlphaFold monomer V2.0 prediction for iron-sulfur clusters transporter ATM1… · a predicted model of the same protein · chain B against A, TM-score 0.87
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 P40416
- Elsewhere: RCSB PDB 7PSM · PDBe 7PSM · UniProt P40416
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