MolNFT v1 · #96149 · protein
1.95 ångström crystal structure of gamma-glutamyl phosphate reductase from saccharomonospora viridis.
4JBE: “1.95 ångström crystal structure of gamma-glutamyl phosphate reductase from saccharomonospora viridis.”. X-ray diffraction, 2 ligands (CA, CL), 9 pockets (best druggability 0.81). MolNFT v1 #96149 on GenesisL1: 3D structure, binding…
- PDB
- 4JBE
- Type
- protein
- Length
- 823 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyl phosphate reductase
- UniProt
- C7MW73
- Ligands
- CA, CL
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-glutamyl phosphate reductase | protein | 411 | 48% helix, 19% strand | C7MW73 |
| B | Gamma-glutamyl phosphate reductase | protein | 412 | 48% helix, 19% strand | C7MW73 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B
- CL · Chloride ion · ion · 12 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.81 | 0.82 | 112 | CA |
| 2 | 708 | 0.71 | 0.78 | 64 | CL, BME |
| 3 | 575 | 0.69 | 0.78 | 43 | CL, BME, EDO |
| 4 | 50 | 0.65 | 0.95 | 15 | empty |
| 5 | 72 | 0.63 | 0.91 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2424 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 2 covalent (engineered, additive adduct).
Compared structures
- 4JBE · 1.95 Angstrom Crystal Structure of Gamma-glutamyl phosphate Reductase from… · the same entry in another collection · chain A 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 C7MW73
- Elsewhere: RCSB PDB 4JBE · PDBe 4JBE · UniProt C7MW73
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