Research workbench
Structural characterization for the nucleotide binding ability of subunit a with AMP-pnp of the A1AO ATP synthase
Analyse Structural characterization for the nucleotide binding ability of subunit a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I4L
- Type
- protein
- Length
- 524 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A-type ATP synthase catalytic subunit a
- EC
- 3.6.3.14
- UniProt
- O57728
- Ligands
- ANP
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A-type ATP synthase catalytic subunit a (EC 3.6.3.14) | protein | 524 | 33% helix, 18% strand | O57728 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A
- ACY · Acetic acid · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.79 | 0.80 | 90 | empty |
| 2 | 153 | 0.52 | 0.79 | 26 | MPD |
| 3 | 50 | 0.45 | 0.84 | 18 | ANP |
| 4 | 70 | 0.42 | 0.80 | 15 | empty |
| 5 | 62 | 0.33 | 0.76 | 12 | ANP |
Compared structures
- 3I4L · Structural characterization for the nucleotide binding ability of subunit A with AMP-PNP… · the same entry in another collection · chain A against A, TM-score 1.00
- O57728 · AlphaFold monomer V2.0 prediction for V-type ATP synthase alpha chain (O57728) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 O57728
- Elsewhere: RCSB PDB 3I4L · PDBe 3I4L · UniProt O57728
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