MolNFT v1 · #16998 · protein
Glutamate synthase from synechocystis sp in complex with 2-oxoglutarate and L-don at 2.45 ångström resolution
1OFE · Ferredoxin-dependent glutamate synthase 2: “Glutamate synthase from synechocystis sp in complex with 2-oxoglutarate and L-don at 2.45 ångström resolution”. X-ray diffraction, 4 ligands (FMN, F3S, AKG), 20 pockets (best druggability…
- PDB
- 1OFE
- Type
- protein
- Length
- 2,970 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferredoxin-dependent glutamate synthase 2
- EC
- 1.4.7.1
- UniProt
- P55038
- Ligands
- FMN, F3S, AKG, ONL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ferredoxin-dependent glutamate synthase 2 (EC 1.4.7.1) | protein | 1485 | 37% helix, 18% strand | P55038 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, B
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- ONL · 5-oxo-L-norleucine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.82 | 0.95 | 49 | FMN, AKG |
| 2 | 176 | 0.82 | 0.97 | 30 | empty |
| 3 | 177 | 0.82 | 0.96 | 36 | empty |
| 4 | 217 | 0.81 | 0.95 | 51 | FMN, AKG |
| 5 | 61 | 0.72 | 0.98 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 61 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1OFE · Glutamate Synthase from Synechocystis sp in complex with 2-Oxoglutarate and L-DON at 2.45… · the same entry in another collection · chain A against A, TM-score 1.00
- P55038 · AlphaFold monomer V2.0 prediction for ferredoxin-dependent glutamate synthase 2 (P55038) · a predicted model of the same protein · chain B 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 P55038
- Elsewhere: RCSB PDB 1OFE · PDBe 1OFE · UniProt P55038
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