Research workbench
Crystal structure of homolog of F420-0:GAMMA-glutamyl ligase from archaeoglobus fulgidus reveals a novel fold.
Analyse Crystal structure of homolog of F420-0:GAMMA-glutamyl ligase from archaeoglobus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2G9I
- Type
- protein
- Length
- 465 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F420-0:GAMMA-glutamyl ligase
- EC
- 6.3.2.-
- UniProt
- O28028
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | F420-0:GAMMA-glutamyl ligase (EC 6.3.2.-) | protein | 233 | 34% helix, 27% strand | O28028 |
| B | F420-0:GAMMA-glutamyl ligase (EC 6.3.2.-) | protein | 232 | 34% helix, 26% strand | O28028 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.77 | 0.79 | 132 | empty |
| 2 | 69 | 0.37 | 0.77 | 12 | empty |
| 3 | 55 | 0.34 | 0.77 | 12 | empty |
| 4 | 55 | 0.26 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2572 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 2G9I · Crystal structure of homolog of F420-0:gamma-Glutamyl Ligase from Archaeoglobus fulgidus… · the same entry in another collection · chain A against A, TM-score 1.00
- O28028 · AlphaFold monomer V2.0 prediction for coenzyme F420:L-glutamate ligase (O28028) · 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 O28028
- Elsewhere: RCSB PDB 2G9I · PDBe 2G9I · UniProt O28028
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