Research workbench
Structure of azospirillum brasilense glutamate synthase in A4B4 oligomeric state.
Analyse Structure of azospirillum brasilense glutamate synthase in A4B4 oligomeric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S6S
- Type
- protein
- Length
- 7,752 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate synthase [NADPH] large chain; Glutamate synthase [NADPH] small chain
- EC
- 1.4.1.13
- UniProt
- Q05755, Q05756
- Ligands
- SF4, FMN, F3S, FAD
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutamate synthase [NADPH] large chain (EC 1.4.1.13) | protein | 1468 | 35% helix, 16% strand | Q05755 |
| G, E, F, H | Glutamate synthase [NADPH] small chain (EC 1.4.1.13) | protein | 470 | 36% helix, 14% strand | Q05756 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 8 copies · chains G, E, F, H
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- F3S · FE3-S4 cluster · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains G, E, F, H
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 | 663 | 0.87 | 0.92 | 99 | FMN |
| 2 | 478 | 0.86 | 0.93 | 96 | FMN |
| 3 | 1063 | 0.86 | 0.86 | 108 | FAD |
| 4 | 1099 | 0.85 | 0.86 | 113 | FAD |
| 5 | 1034 | 0.85 | 0.85 | 111 | FAD |
Interfaces
10 interfaces between chains.
- A–C · 2087 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 2081 Ų buried · 18 hydrogen bonds · protein-protein
- D–H · 1215 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 1167 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 1165 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 covalent (covalent ligand).
Compared structures
- 6S6S · Structure of Azospirillum brasilense Glutamate Synthase in a4b4 oligomeric state. · the same entry in another collection · chain H against H, TM-score 1.00
- Q05755 · AlphaFold monomer V2.0 prediction for glutamate synthase [NADPH] large chain (Q05755) · a predicted model of the same protein · chain A 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 Q05755
- Every structure of UniProt Q05756
- Elsewhere: RCSB PDB 6S6S · PDBe 6S6S · UniProt Q05755 · UniProt Q05756
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