MolNFT v1 · #51637 · protein
The 9.5 a resolution structure of glutamate synthase from cryo- electron microscopy and its oligomerization behavior in solution: functional implications.
2VDC · Glutamate synthase [NADPH] large chain: “The 9.5 a resolution structure of glutamate synthase from cryo- electron microscopy and its oligomerization…”. Electron microscopy, 6 ligands (SF4, OMT, FMN), 20 pockets (best druggability…
- PDB
- 2VDC
- Type
- protein
- Length
- 11,568 residues
- Chains
- 12
- 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, OMT, FMN, AKG, F3S, FAD
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutamate synthase [NADPH] large chain (EC 1.4.1.13) | protein | 1472 | 37% helix, 17% strand | Q05755 |
| G, H, I, J, K, L | Glutamate synthase [NADPH] small chain (EC 1.4.1.13) | protein | 456 | 36% helix, 17% strand | Q05756 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 12 copies · chains G, H, I, J, K, L
- OMT · S-dioxymethionine · ligand · 6 copies · chains A, B, C, D, E, F
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, D, E, F
- F3S · FE3-S4 cluster · ligand · 6 copies · chains A, J, B, G, C, K, D, H, E, L, F, I
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains G, H, I, J, K, L
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 | 401 | 0.86 | 0.94 | 73 | FMN, AKG |
| 2 | 394 | 0.85 | 0.93 | 72 | FMN, AKG |
| 3 | 398 | 0.84 | 0.93 | 71 | FMN, AKG |
| 4 | 432 | 0.84 | 0.92 | 79 | FMN, AKG |
| 5 | 412 | 0.84 | 0.92 | 72 | FMN, AKG |
Interfaces
21 interfaces between chains.
- E–F · 2392 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2383 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2379 Ų buried · 38 hydrogen bonds · protein-protein
- C–K · 1004 Ų buried · 27 hydrogen bonds · protein-protein
- E–L · 1002 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2VDC · The 9.5 a resolution structure of glutamate synthase from cryo-electron microscopy and… · the same entry in another collection · chain L against L, 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 Q05755
- Every structure of UniProt Q05756
- Elsewhere: RCSB PDB 2VDC · PDBe 2VDC · UniProt Q05755 · UniProt Q05756
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