MolNFT v1 · #144993 · protein
Aminoglycoside phosphotransferase (2'')-ia in complex with gmppnp, magnesium, and dibekacin
6CAV · Bifunctional AAC/APH: “Aminoglycoside phosphotransferase (2'')-ia in complex with gmppnp, magnesium, and dibekacin”. X-ray diffraction, 4 ligands (GNP, 84D, MG), 8 pockets (best druggability 0.77). MolNFT v1 #144993 on GenesisL1: 3D…
- PDB
- 6CAV
- Type
- protein
- Length
- 1,149 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional AAC/APH
- EC
- 2.3.1.-, 2.7.1.190
- UniProt
- P0A0C1
- Ligands
- GNP, 84D, MG, CL
- Pockets
- 8 · best druggability 0.77
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.-, 2.7.1.190) | protein | 288 | 51% helix, 17% strand | P0A0C1 |
| B | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.190) | protein | 292 | 50% helix, 17% strand | P0A0C1 |
| C | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.190) | protein | 285 | 50% helix, 17% strand | P0A0C1 |
| D | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.190) | protein | 284 | 51% helix, 17% strand | P0A0C1 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
- 84D · Dibekacin · 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 | 1117 | 0.77 | 0.79 | 102 | empty |
| 2 | 905 | 0.72 | 0.76 | 74 | GNP, MG, 84D |
| 3 | 617 | 0.67 | 0.76 | 63 | GNP, MG, 84D |
| 4 | 414 | 0.64 | 0.78 | 49 | 84D |
| 5 | 315 | 0.60 | 0.77 | 37 | 84D |
Interfaces
5 interfaces between chains.
- A–B · 756 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 595 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 243 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 173 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CAV · Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and… · 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 A 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 6CAV · PDBe 6CAV · UniProt P0A0C1
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