Research workbench
Phosphoribosylamine-glycine ligase from yersinia pestis
Analyse Phosphoribosylamine-glycine ligase from yersinia pestis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MJF
- Type
- protein
- Length
- 429 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylamine--glycine ligase
- EC
- 6.3.4.13
- UniProt
- Q8ZAR2
- Ligands
- NA, SO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylamine--glycine ligase (EC 6.3.4.13) | protein | 429 | 33% helix, 28% strand | Q8ZAR2 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- PGE · Triethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.66 | 0.78 | 37 | GOL |
| 2 | 148 | 0.53 | 0.80 | 27 | empty |
| 3 | 211 | 0.46 | 0.74 | 27 | SO4 |
| 4 | 52 | 0.23 | 0.71 | 13 | EDO, SO4 |
Modifications
Observed in the structure: 11 modified, 1 covalent (engineered, additive adduct).
Compared structures
- 3MJF · Phosphoribosylamine-glycine ligase from Yersinia pestis · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZAR2 · AlphaFold monomer V2.0 prediction for phosphoribosylamine--glycine ligase (Q8ZAR2) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q8ZAR2
- Elsewhere: RCSB PDB 3MJF · PDBe 3MJF · UniProt Q8ZAR2
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