Research workbench
Ethylene forming enzyme in complex with manganese and 2-oxoglutarate
Analyse Ethylene forming enzyme in complex with manganese and 2-oxoglutarate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V2X
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-oxoglutarate-dependent ETHYLENE/SUCCINATE-forming enzyme
- EC
- 1.13.12.19, 1.14.11.34
- UniProt
- P32021
- Ligands
- AKG, MN
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-oxoglutarate-dependent ETHYLENE/SUCCINATE-forming enzyme (EC 1.13.12.19, 1.14.11.34) | protein | 345 | 31% helix, 19% strand | P32021 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.77 | 0.79 | 115 | MN, AKG |
| 2 | 396 | 0.75 | 0.85 | 62 | MN, AKG |
| 3 | 94 | 0.36 | 0.75 | 20 | empty |
| 4 | 63 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 226 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5V2X · Ethylene forming enzyme in complex with manganese and 2-oxoglutarate · the same entry in another collection · chain A against A, TM-score 1.00
- P32021 · AlphaFold monomer V2.0 prediction for 2-oxoglutarate-dependent ETHYLENE/SUCCINATE-forming… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P32021
- Elsewhere: RCSB PDB 5V2X · PDBe 5V2X · UniProt P32021
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