Research workbench
Aminoglycoside phosphotransferase (2'')-ia (ctd of AAC(6')- IE/APH(2'')-ia) S214A mutant in complex with gmppnp and magnesium
Analyse Aminoglycoside phosphotransferase (2'')-ia (ctd of AAC(6')- IE/APH(2'')-ia)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IQH
- Type
- protein
- Length
- 1,166 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, MG, CL
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-) | protein | 294 | 50% helix, 17% strand | P0A0C1 |
| B | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-) | protein | 293 | 51% helix, 17% strand | P0A0C1 |
| C | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-) | protein | 288 | 51% helix, 17% strand | P0A0C1 |
| D | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-) | protein | 291 | 50% helix, 17% strand | P0A0C1 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.74 | 0.81 | 59 | empty |
| 2 | 906 | 0.71 | 0.75 | 84 | GNP, MG |
| 3 | 734 | 0.70 | 0.77 | 72 | GNP, MG |
| 4 | 161 | 0.58 | 0.82 | 25 | empty |
| 5 | 258 | 0.57 | 0.78 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–B · 718 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 708 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 210 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 142 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5IQH · Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) S214A mutant… · 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 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 P0A0C1
- Elsewhere: RCSB PDB 5IQH · PDBe 5IQH · UniProt P0A0C1
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