Research workbench
Ethylene forming enzyme in complex with manganese, 2-oxoglutarate and N-omega-hydroxy-L-arginine
Analyse Ethylene forming enzyme in complex with manganese, 2-oxoglutarate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VKA
- Type
- protein
- Length
- 348 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.169
- Source
- Pseudomonas savastanoi pv. phaseolicola
- Molecule
- 2-oxoglutarate-dependent ethylene/succinate-forming enzyme
- EC
- 1.13.12.19, 1.14.11.34
- UniProt
- P32021
- Ligands
- AKG, HAR, MN
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.169 · 1 distinct chain · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoglutarate-dependent ethylene/succinate-forming enzyme (EC 1.13.12.19, 1.14.11.34) | protein | 348 | 33% helix, 19% strand | P32021 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- HAR · N-omega-hydroxy-L-arginine · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.74 | 0.97 | 27 | MN, AKG |
| 2 | 102 | 0.38 | 0.75 | 17 | empty |
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5VKA · Ethylene forming enzyme in complex with manganese, 2-oxoglutarate and… · 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 A against A, TM-score 0.97
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 5VKA · PDBe 5VKA · UniProt P32021
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