Research workbench
Crystal structure of mtpap in complex with atpgammas
Analyse Crystal structure of mtpap in complex with atpgammas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A2W
- Type
- protein
- Length
- 935 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial protein
- UniProt
- F1NBW0
- Ligands
- AGS, MG
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial protein | protein | 468 | 40% helix, 17% strand | F1NBW0 |
| B | Mitochondrial protein | protein | 467 | 40% helix, 18% strand | F1NBW0 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 3 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.73 | 0.76 | 92 | AGS, PEG |
| 2 | 640 | 0.67 | 0.76 | 50 | AGS, MG, PEG |
| 3 | 279 | 0.51 | 0.74 | 32 | empty |
| 4 | 158 | 0.49 | 0.77 | 25 | empty |
| 5 | 114 | 0.46 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3441 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 5A2W · Crystal structure of mtPAP in complex with ATPgammaS · 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 F1NBW0
- Elsewhere: RCSB PDB 5A2W · PDBe 5A2W · UniProt F1NBW0
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