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Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor tyrphostin AG1478
Analyse Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FEX
- Type
- protein
- Length
- 1,283 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.71
- Source
- Acinetobacter baumannii
- Molecule
- Aminoglycoside 3'-phosphotransferase AphA1-IAB
- EC
- 2.7.1.95
- UniProt
- B0VD92
- Ligands
- KAN, 0TO, NA
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.71 · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Aminoglycoside 3'-phosphotransferase AphA1-IAB (EC 2.7.1.95) | protein | 254 | 44% helix, 20% strand | B0VD92 |
| B | Aminoglycoside 3'-phosphotransferase AphA1-IAB (EC 2.7.1.95) | protein | 261 | 42% helix, 20% strand | B0VD92 |
| C | Aminoglycoside 3'-phosphotransferase AphA1-IAB (EC 2.7.1.95) | protein | 261 | 43% helix, 19% strand | B0VD92 |
| D | Aminoglycoside 3'-phosphotransferase AphA1-IAB (EC 2.7.1.95) | protein | 253 | 41% helix, 20% strand | B0VD92 |
Ligands and binding sites
- KAN · Kanamycin A · ligand · 5 copies · chains A, B, E, C, D
- 0TO · N-(3-chlorophenyl)-6,7-dimethoxyquinazolin-4-amine · ligand · 4 copies · chains A, B, C, D, E
- NA · Sodium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.78 | 0.80 | 81 | KAN, 0TO |
| 2 | 392 | 0.72 | 0.83 | 41 | KAN |
| 3 | 388 | 0.71 | 0.83 | 43 | KAN |
| 4 | 504 | 0.67 | 0.78 | 50 | KAN, 0TO |
| 5 | 651 | 0.67 | 0.76 | 72 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1676 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1487 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 669 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 652 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4FEX · Crystal structure of the aminoglycoside phosphotransferase APH(3')-ia, with substrate… · 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 B0VD92
- Elsewhere: RCSB PDB 4FEX · PDBe 4FEX · UniProt B0VD92
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