MolNFT v1 · #141875 · protein
FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase anda
5ZM2: “FE(II)/(ALPHA)KETOGLUTARATE-dependent dioxygenase anda”. X-ray diffraction, 10 pockets (best druggability 0.77). MolNFT v1 #141875 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZM2
- Type
- protein
- Length
- 1,075 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dioxygenase anda
- EC
- 1.14.11.-
- UniProt
- A0A097ZPD5
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dioxygenase anda (EC 1.14.11.-) | protein | 267 | 28% helix, 26% strand | A0A097ZPD5 |
| B | Dioxygenase anda (EC 1.14.11.-) | protein | 268 | 28% helix, 26% strand | A0A097ZPD5 |
| C | Dioxygenase anda (EC 1.14.11.-) | protein | 269 | 29% helix, 25% strand | A0A097ZPD5 |
| D | Dioxygenase anda (EC 1.14.11.-) | protein | 271 | 28% helix, 25% strand | A0A097ZPD5 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.77 | 0.91 | 38 | empty |
| 2 | 653 | 0.72 | 0.79 | 73 | empty |
| 3 | 571 | 0.70 | 0.79 | 48 | empty |
| 4 | 256 | 0.62 | 0.81 | 31 | empty |
| 5 | 293 | 0.61 | 0.79 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1703 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 258 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 248 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ZM2 · Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AndA · 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 5ZM2 · PDBe 5ZM2 · UniProt A0A097ZPD5
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