Research workbench
Crystal structure of the phosphotransferase domain of the bifunctional aminoglycoside resistance enzyme AAC(6')-ie-APH(2'')-ia
Analyse Crystal structure of the phosphotransferase domain of the bifunctional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ORK
- Type
- protein
- Length
- 1,183 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.-
- UniProt
- P0A0C1
- Ligands
- GDP, MG
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-) | protein | 299 | 50% helix, 16% strand | P0A0C1 |
| B | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-) | protein | 296 | 51% helix, 17% strand | P0A0C1 |
| C | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-) | protein | 293 | 52% helix, 17% strand | P0A0C1 |
| D | Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-) | protein | 295 | 49% helix, 15% strand | P0A0C1 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.80 | 0.82 | 78 | GDP, MG |
| 2 | 892 | 0.78 | 0.81 | 79 | GDP, MG |
| 3 | 913 | 0.75 | 0.79 | 91 | empty |
| 4 | 986 | 0.74 | 0.77 | 73 | GDP, MG |
| 5 | 981 | 0.74 | 0.77 | 76 | GDP, MG |
Interfaces
5 interfaces between chains.
- A–D · 802 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 793 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 467 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 433 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 31 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ORK · Crystal Structure of the Phosphotransferase Domain of the Bifunctional Aminoglycoside… · 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 C 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 4ORK · PDBe 4ORK · UniProt P0A0C1
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