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Crystal structure of aminoglycoside phosphotransferase aph (3')-iiia in complex with the inhibitor AR_3A
Analyse Crystal structure of aminoglycoside phosphotransferase aph (3')-iiia in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BKK
- Type
- protein
- Length
- 820 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoglycoside 3'-phosphotransferase; Designed ankyrin repeat inhibitor AR_3A
- EC
- 2.7.1.95
- UniProt
- P00554
- Ligands
- ADP, MG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoglycoside 3'-phosphotransferase (EC 2.7.1.95) | protein | 247 | 36% helix, 21% strand | P00554 |
| B | Designed ankyrin repeat inhibitor AR_3A | protein | 155 | 50% helix, 0% strand | — |
| C | Aminoglycoside 3'-phosphotransferase (EC 2.7.1.95) | protein | 262 | 39% helix, 21% strand | P00554 |
| D | Designed ankyrin repeat inhibitor AR_3A | protein | 156 | 48% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 4 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.78 | 0.83 | 74 | ADP, MG |
| 2 | 432 | 0.69 | 0.81 | 55 | empty |
| 3 | 401 | 0.66 | 0.79 | 46 | empty |
| 4 | 258 | 0.61 | 0.80 | 42 | ADP, MG |
| 5 | 200 | 0.52 | 0.77 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1008 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 950 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 316 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 116 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2BKK · Crystal structure of Aminoglycoside Phosphotransferase APH(3')-IIIa in complex with the… · 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 P00554
- Elsewhere: RCSB PDB 2BKK · PDBe 2BKK · UniProt P00554
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