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Crystal structure of an amide bond forming F420-gamma glutamyl ligase from archaeoglobus fulgidus
Analyse Crystal structure of an amide bond forming F420-gamma glutamyl ligase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PHN
- Type
- protein
- Length
- 497 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
- Ligands
- GDP, MN
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | F420-0:GAMMA-glutamyl ligase (EC 6.3.2.-) | protein | 248 | 32% helix, 27% strand | O28028 |
| B | F420-0:GAMMA-glutamyl ligase (EC 6.3.2.-) | protein | 249 | 32% helix, 27% strand | O28028 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.85 | 0.86 | 137 | MN, ACT, GDP, EDO |
| 2 | 71 | 0.36 | 0.77 | 13 | empty |
| 3 | 83 | 0.36 | 0.75 | 17 | EDO |
| 4 | 82 | 0.36 | 0.75 | 16 | EDO |
| 5 | 58 | 0.33 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 3848 Ų buried · 75 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2PHN · Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus… · 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 0.98
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 2PHN · PDBe 2PHN · UniProt O28028
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