MolNFT v1 · #137300 · protein
Ethylene forming enzyme in complex with manganese, 2-oxoglutarate and argininamide
5VKB · 2-oxoglutarate-dependent ETHYLENE/SUCCINATE-forming enzyme: “Ethylene forming enzyme in complex with manganese, 2-oxoglutarate and argininamide”. X-ray diffraction, 3 ligands (AKG, AAR, MN), 4 pockets (best druggability 0.72).…
- PDB
- 5VKB
- Type
- protein
- Length
- 347 residues
- Chains
- 1
- 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, AAR, MN
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 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 | 347 | 33% helix, 19% strand | P32021 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- AAR · Arginineamide · 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
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 | 125 | 0.72 | 0.92 | 38 | AKG |
| 2 | 50 | 0.58 | 0.91 | 19 | AAR |
| 3 | 114 | 0.41 | 0.76 | 17 | empty |
| 4 | 62 | 0.30 | 0.74 | 19 | empty |
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5VKB · Ethylene forming enzyme in complex with manganese, 2-oxoglutarate and argininamide · 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 5VKB · PDBe 5VKB · UniProt P32021
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