Research workbench
FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase anda with preandiloid B
Analyse FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase anda with preandiloid B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZM3
- Type
- protein
- Length
- 1,142 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dioxygenase anda
- EC
- 1.14.11.-
- UniProt
- A0A097ZPD5
- Ligands
- AKG, 9FR, FE
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dioxygenase anda (EC 1.14.11.-) | protein | 285 | 28% helix, 23% strand | A0A097ZPD5 |
| B | Dioxygenase anda (EC 1.14.11.-) | protein | 286 | 27% helix, 22% strand | A0A097ZPD5 |
| C | Dioxygenase anda (EC 1.14.11.-) | protein | 286 | 27% helix, 22% strand | A0A097ZPD5 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- 9FR · (6as,8ar,12as,12br,13ar)-5,6A,9,9,12A,13A-hexamethyl-7, 8,8A,9,11,12,12A,12B,13,13A-decahydro-3H-benzo[a]furo[3,4-j]xanthene-3,4,10(1h,6ah)-trione · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.79 | 0.87 | 42 | AKG, 9FR |
| 2 | 462 | 0.79 | 0.87 | 41 | FE, AKG, 9FR |
| 3 | 470 | 0.78 | 0.86 | 45 | FE, AKG, 9FR |
| 4 | 467 | 0.78 | 0.86 | 44 | FE, AKG, 9FR |
| 5 | 286 | 0.55 | 0.76 | 41 | empty |
Interfaces
4 interfaces between chains.
- A–B · 369 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 314 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 284 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 92 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5ZM3 · Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid B · 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 A0A097ZPD5
- Elsewhere: RCSB PDB 5ZM3 · PDBe 5ZM3 · UniProt A0A097ZPD5
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