MolNFT v1 · #66805 · protein
Crystal structure of apo spectinomycin phosphotransferase, APH(9)-ia
3I1A: “Crystal structure of apo spectinomycin phosphotransferase, APH(9)-ia”. X-ray diffraction, 9 pockets (best druggability 0.61). MolNFT v1 #66805 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3I1A
- Type
- protein
- Length
- 657 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spectinomycin phosphotransferase
- UniProt
- O06916
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spectinomycin phosphotransferase | protein | 328 | 46% helix, 13% strand | O06916 |
| B | Spectinomycin phosphotransferase | protein | 329 | 45% helix, 13% strand | O06916 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.61 | 0.77 | 33 | MES |
| 2 | 274 | 0.60 | 0.78 | 27 | MES |
| 3 | 119 | 0.54 | 0.83 | 25 | empty |
| 4 | 171 | 0.51 | 0.79 | 22 | empty |
| 5 | 138 | 0.48 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 514 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3I1A · Crystal Structure of apo Spectinomycin Phosphotransferase, APH(9)-Ia · 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 O06916
- Elsewhere: RCSB PDB 3I1A · PDBe 3I1A · UniProt O06916
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