MolNFT v1 · #126167 · protein
Ethylene forming enzyme from pseudomonas syringae pv. phaseolicola - P1 ultra-high resolution crystal form in complex with iron, N- oxalylglycine and arginine
5LUN · 2-oxoglutarate-dependent ETHYLENE/SUCCINATE-forming enzyme: “Ethylene forming enzyme from pseudomonas syringae pv. phaseolicola - P1 ultra-high resolution crystal form in…”. X-ray diffraction, 3 ligands (OGA, ARG, FE), 15 pockets…
- PDB
- 5LUN
- Type
- protein
- Length
- 1,358 residues
- Chains
- 4
- 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
- OGA, ARG, FE
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 32% 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 | 338 | 33% helix, 20% strand | P32021 |
| B | 2-oxoglutarate-dependent ETHYLENE/SUCCINATE-forming enzyme (EC 1.13.12.19, 1.14.11.34) | protein | 339 | 32% helix, 19% strand | P32021 |
| C | 2-oxoglutarate-dependent ETHYLENE/SUCCINATE-forming enzyme (EC 1.13.12.19, 1.14.11.34) | protein | 340 | 32% helix, 19% strand | P32021 |
| D | 2-oxoglutarate-dependent ETHYLENE/SUCCINATE-forming enzyme (EC 1.13.12.19, 1.14.11.34) | protein | 341 | 31% helix, 19% strand | P32021 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 4 copies · chains A, B, C, D
- ARG · Arginine · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.76 | 0.96 | 33 | FE, OGA, ARG |
| 2 | 960 | 0.76 | 0.79 | 95 | ARG |
| 3 | 90 | 0.75 | 0.97 | 28 | OGA |
| 4 | 91 | 0.75 | 0.97 | 28 | FE, OGA |
| 5 | 705 | 0.75 | 0.80 | 82 | ARG |
Interfaces
5 interfaces between chains.
- C–D · 414 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 410 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 401 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 385 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 108 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5LUN · Ethylene Forming Enzyme from Pseudomonas syringae pv. phaseolicola - P1 ultra-high… · the same entry in another collection · chain D against D, 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 0.99
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 5LUN · PDBe 5LUN · UniProt P32021
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