MolNFT v1 · #123503 · protein
The structure of ATP-bound aerobactin synthetase iuca from a hypervirulent pathotype of klebsiella pneumoniae
5JM8 · Aerobactin synthase iuca: “The structure of ATP-bound aerobactin synthetase iuca from a hypervirulent pathotype of klebsiella pneumoniae”. X-ray diffraction, 2 ligands (ATP, MG), 20 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 5JM8
- Type
- protein
- Length
- 4,421 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aerobactin synthase iuca
- UniProt
- A0A0X9V8F4
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aerobactin synthase iuca | protein | 556 | 43% helix, 22% strand | A0A0X9V8F4 |
| C | Aerobactin synthase iuca | protein | 552 | 45% helix, 23% strand | A0A0X9V8F4 |
| D | Aerobactin synthase iuca | protein | 552 | 44% helix, 23% strand | A0A0X9V8F4 |
| E, G | Aerobactin synthase iuca | protein | 552 | 44% helix, 22% strand | A0A0X9V8F4 |
| F | Aerobactin synthase iuca | protein | 551 | 44% helix, 21% strand | A0A0X9V8F4 |
| H | Aerobactin synthase iuca | protein | 550 | 43% helix, 21% strand | A0A0X9V8F4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.82 | 0.85 | 90 | ATP |
| 2 | 843 | 0.81 | 0.84 | 90 | ATP |
| 3 | 875 | 0.81 | 0.83 | 91 | ATP |
| 4 | 783 | 0.81 | 0.84 | 90 | ATP, MG |
| 5 | 583 | 0.77 | 0.84 | 65 | ATP, MG |
Interfaces
14 interfaces between chains.
- A–E · 901 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 877 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 844 Ų buried · 6 hydrogen bonds · protein-protein
- D–H · 818 Ų buried · 6 hydrogen bonds · protein-protein
- A–G · 680 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5JM8 · The structure of ATP-bound aerobactin synthetase IucA from a hypervirulent pathotype of… · 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 A0A0X9V8F4
- Elsewhere: RCSB PDB 5JM8 · PDBe 5JM8 · UniProt A0A0X9V8F4
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