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Octameric structure of the phosphoribosylaminoimidazole carboxylase catalytic subunit from francisella tularensis subsp. tularensis schu S4.
Analyse Octameric structure of the phosphoribosylaminoimidazole carboxylase catalytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OOW
- Type
- protein
- Length
- 1,287 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylaminoimidazole CARBOXYLASE,CATALYTIC subunit
- EC
- 4.1.1.21
- UniProt
- Q5NGE9
- Ligands
- PO4, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Phosphoribosylaminoimidazole CARBOXYLASE,CATALYTIC subunit (EC 4.1.1.21) | protein | 160 | 49% helix, 16% strand | Q5NGE9 |
| B | Phosphoribosylaminoimidazole CARBOXYLASE,CATALYTIC subunit (EC 4.1.1.21) | protein | 162 | 49% helix, 17% strand | Q5NGE9 |
| C, H | Phosphoribosylaminoimidazole CARBOXYLASE,CATALYTIC subunit (EC 4.1.1.21) | protein | 161 | 48% helix, 14% strand | Q5NGE9 |
| D, F | Phosphoribosylaminoimidazole CARBOXYLASE,CATALYTIC subunit (EC 4.1.1.21) | protein | 162 | 48% helix, 16% strand | Q5NGE9 |
| G | Phosphoribosylaminoimidazole CARBOXYLASE,CATALYTIC subunit (EC 4.1.1.21) | protein | 159 | 50% helix, 16% strand | Q5NGE9 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 17 copies · chains A, G, B, D, C, H, E, F
- CL · Chloride ion · ion · 14 copies · chains A, F, B, C, D, E, G, H
- FMT · Formic acid · additive · 13 copies · chains A, B, C, F, D, E, G, H
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains B, C, D, H, E, F, A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.84 | 0.88 | 62 | MPD |
| 2 | 296 | 0.66 | 0.82 | 38 | CL, PO4 |
| 3 | 125 | 0.62 | 0.87 | 29 | empty |
| 4 | 346 | 0.62 | 0.78 | 45 | CL, PO4, FMT |
| 5 | 126 | 0.62 | 0.86 | 28 | empty |
Interfaces
16 interfaces between chains.
- F–G · 1557 Ų buried · 30 hydrogen bonds · protein-protein
- A–H · 1557 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1553 Ų buried · 27 hydrogen bonds · protein-protein
- B–E · 1547 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1081 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 modified (engineered).
Compared structures
- 3OOW · Octameric structure of the phosphoribosylaminoimidazole carboxylase catalytic subunit… · 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 Q5NGE9
- Elsewhere: RCSB PDB 3OOW · PDBe 3OOW · UniProt Q5NGE9
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