Research workbench
Aminoglycoside phosphotransferase (2'')-ia in complex with gmppnp, magnesium, and amikacin
Analyse Aminoglycoside phosphotransferase (2'')-ia in complex with gmppnp, magnesium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CGD
- Type
- protein
- Length
- 1,189 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, AKN, MG, CL
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.190) | protein | 298 | 51% helix, 17% strand | P0A0C1 |
| B | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.190) | protein | 297 | 51% helix, 16% strand | P0A0C1 |
| C | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.190) | protein | 296 | 51% helix, 16% strand | P0A0C1 |
| D | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.190) | protein | 298 | 50% helix, 16% strand | P0A0C1 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
- AKN · (2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide · ligand · 2 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.77 | 0.79 | 99 | empty |
| 2 | 1108 | 0.73 | 0.76 | 75 | GNP, AKN, MG |
| 3 | 856 | 0.71 | 0.76 | 72 | GNP, AKN, MG |
| 4 | 824 | 0.70 | 0.76 | 70 | GNP, MG |
| 5 | 649 | 0.68 | 0.76 | 71 | GNP, MG |
Interfaces
5 interfaces between chains.
- A–B · 872 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 859 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 235 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 137 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CGD · Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Amikacin · 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 6CGD · PDBe 6CGD · UniProt P0A0C1
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