Research workbench
FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase anda with preandiloid C
Analyse FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase anda with preandiloid C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZM4
- Type
- protein
- Length
- 1,140 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, 9FU, FE
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dioxygenase anda (EC 1.14.11.-) | protein | 285 | 28% helix, 23% strand | A0A097ZPD5 |
| B | Dioxygenase anda (EC 1.14.11.-) | protein | 284 | 28% helix, 23% strand | A0A097ZPD5 |
| C | Dioxygenase anda (EC 1.14.11.-) | protein | 285 | 28% helix, 23% strand | A0A097ZPD5 |
| D | Dioxygenase anda (EC 1.14.11.-) | protein | 286 | 28% helix, 22% strand | A0A097ZPD5 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- 9FU · (6as,8ar,12as,12br,13ar)-5,6A,9,9,12A,13A-hexamethyl-7, 8,8A,9,12A,12B,13,13A-octahydro-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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.85 | 0.94 | 41 | FE, AKG, 9FU |
| 2 | 352 | 0.85 | 0.94 | 38 | FE, AKG, 9FU |
| 3 | 520 | 0.78 | 0.85 | 54 | FE, AKG, 9FU |
| 4 | 429 | 0.77 | 0.86 | 37 | FE, AKG, 9FU |
| 5 | 216 | 0.77 | 0.91 | 49 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2252 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 372 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 295 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 75 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5ZM4 · Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA with preandiloid C · the same entry in another collection · chain B against B, 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 5ZM4 · PDBe 5ZM4 · UniProt A0A097ZPD5
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