MolNFT v1 · #122479 · protein
Aminoglycoside phosphotransferase (2'')-ia (ctd of AAC(6')- IE/APH(2'')-ia) in complex with gmppnp, magnesium, and ribostamycin
5IQD · Bifunctional AAC/APH: “Aminoglycoside phosphotransferase (2'')-ia (ctd of AAC(6')- IE/APH(2'')-ia) in complex with gmppnp…”. X-ray diffraction, 4 ligands (GNP, RIO, MG), 8 pockets (best druggability 0.76). MolNFT v1 #122479 on…
- PDB
- 5IQD
- Type
- protein
- Length
- 1,184 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional AAC/APH
- EC
- 2.3.1.-, 2.7.1.-
- UniProt
- P0A0C1
- Ligands
- GNP, RIO, MG, CL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-) | protein | 296 | 50% helix, 16% strand | P0A0C1 |
| B | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-) | protein | 299 | 50% helix, 16% strand | P0A0C1 |
| C | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-) | protein | 292 | 50% helix, 16% strand | P0A0C1 |
| D | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-) | protein | 297 | 51% helix, 16% strand | P0A0C1 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
- RIO · Ribostamycin · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.76 | 0.78 | 83 | empty |
| 2 | 1070 | 0.72 | 0.76 | 90 | GNP, RIO, MG |
| 3 | 867 | 0.71 | 0.76 | 67 | GNP, RIO, MG |
| 4 | 605 | 0.67 | 0.77 | 67 | GNP, RIO, MG |
| 5 | 293 | 0.62 | 0.79 | 31 | RIO |
Interfaces
4 interfaces between chains.
- A–B · 934 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 829 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 211 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 123 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5IQD · Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P0A0C1 · AlphaFold monomer V2.0 prediction for bifunctional AAC/APH (P0A0C1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P0A0C1
- Elsewhere: RCSB PDB 5IQD · PDBe 5IQD · UniProt P0A0C1
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