MolNFT v1 · #145179 · protein
Aminoglycoside phosphotransferase (2'')-ia in complex with gmppnp, magnesium, and arbekacin
6CGG · Bifunctional AAC/APH: “Aminoglycoside phosphotransferase (2'')-ia in complex with gmppnp, magnesium, and arbekacin”. X-ray diffraction, 4 ligands (GNP, 84G, MG), 11 pockets (best druggability 0.76). MolNFT v1 #145179 on GenesisL1…
- PDB
- 6CGG
- Type
- protein
- Length
- 1,168 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, 84G, MG, CL
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.190) | protein | 296 | 50% helix, 17% strand | P0A0C1 |
| B | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.190) | protein | 295 | 50% helix, 17% strand | P0A0C1 |
| C | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.190) | protein | 288 | 51% helix, 17% strand | P0A0C1 |
| D | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.190) | protein | 289 | 51% helix, 17% strand | P0A0C1 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
- 84G · Arbekacin · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.76 | 0.79 | 81 | empty |
| 2 | 902 | 0.72 | 0.76 | 73 | GNP, 84G, MG |
| 3 | 965 | 0.72 | 0.76 | 69 | GNP, MG |
| 4 | 636 | 0.69 | 0.77 | 67 | 84G, GNP, MG |
| 5 | 320 | 0.60 | 0.77 | 40 | empty |
Interfaces
5 interfaces between chains.
- A–B · 729 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 659 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 220 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 144 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6CGG · 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 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 6CGG · PDBe 6CGG · UniProt P0A0C1
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