MolNFT v1 · #65911 · protein
Structure of the streptomycin-ATP-APH(2")-iia ternary complex
3HAV · Aminoglycoside phosphotransferase: “Structure of the streptomycin-ATP-APH(2")-iia ternary complex”. X-ray diffraction, 3 ligands (ATP, SRY, MG), 13 pockets (best druggability 0.72). MolNFT v1 #65911 on GenesisL1: 3D structure…
- PDB
- 3HAV
- Type
- protein
- Length
- 877 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoglycoside phosphotransferase
- UniProt
- Q9EVD7
- Ligands
- ATP, SRY, MG
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoglycoside phosphotransferase | protein | 296 | 47% helix, 15% strand | Q9EVD7 |
| B | Aminoglycoside phosphotransferase | protein | 297 | 41% helix, 14% strand | Q9EVD7 |
| C | Aminoglycoside phosphotransferase | protein | 284 | 41% helix, 15% strand | Q9EVD7 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- SRY · Streptomycin · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.72 | 0.76 | 88 | SRY |
| 2 | 418 | 0.68 | 0.80 | 49 | SRY |
| 3 | 353 | 0.65 | 0.80 | 35 | SRY |
| 4 | 449 | 0.64 | 0.77 | 43 | empty |
| 5 | 303 | 0.63 | 0.80 | 40 | empty |
Interfaces
2 interfaces between chains.
- A–C · 626 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 472 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3HAV · Structure of the streptomycin-ATP-APH(2)-IIa ternary complex" · 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 Q9EVD7
- Elsewhere: RCSB PDB 3HAV · PDBe 3HAV · UniProt Q9EVD7
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