MolNFT v1 · #77476 · protein
Crystal structure of treponema denticola pure
3RG8 · Phosphoribosylaminoimidazole carboxylase, pure protein: “Crystal structure of treponema denticola pure”. X-ray diffraction, 20 pockets (best druggability 0.88). MolNFT v1 #77476 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3RG8
- Type
- protein
- Length
- 1,252 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylaminoimidazole carboxylase, pure protein
- EC
- 4.1.1.21
- UniProt
- Q73PV9
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylaminoimidazole carboxylase, pure protein (EC 4.1.1.21) | protein | 155 | 52% helix, 15% strand | Q73PV9 |
| B, D, E, F, H | Phosphoribosylaminoimidazole carboxylase, pure protein (EC 4.1.1.21) | protein | 156 | 53% helix, 15% strand | Q73PV9 |
| C | Phosphoribosylaminoimidazole carboxylase, pure protein (EC 4.1.1.21) | protein | 158 | 53% helix, 15% strand | Q73PV9 |
| G | Phosphoribosylaminoimidazole carboxylase, pure protein (EC 4.1.1.21) | protein | 159 | 53% helix, 14% strand | Q73PV9 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.88 | 0.97 | 39 | empty |
| 2 | 352 | 0.67 | 0.81 | 69 | empty |
| 3 | 494 | 0.66 | 0.77 | 65 | empty |
| 4 | 134 | 0.63 | 0.86 | 32 | EDO |
| 5 | 291 | 0.63 | 0.80 | 46 | empty |
Interfaces
20 interfaces between chains.
- B–F · 1720 Ų buried · 28 hydrogen bonds · protein-protein
- C–G · 1645 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 1637 Ų buried · 26 hydrogen bonds · protein-protein
- D–H · 1637 Ų buried · 29 hydrogen bonds · protein-protein
- B–G · 1291 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
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 Q73PV9
- Elsewhere: RCSB PDB 3RG8 · PDBe 3RG8 · UniProt Q73PV9
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