MolNFT v1 · #114962 · protein
Crystal structure of treponema denticola PURE2-S38D
5C5D · Phosphoribosylaminoimidazole carboxylase: “Crystal structure of treponema denticola PURE2-S38D”. X-ray diffraction, 7 pockets (best druggability 0.57). MolNFT v1 #114962 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5C5D
- Type
- protein
- Length
- 633 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylaminoimidazole carboxylase
- EC
- 4.1.1.21
- UniProt
- Q73PV9
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) | protein | 158 | 52% helix, 15% strand | Q73PV9 |
| B, C | Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) | protein | 158 | 51% helix, 15% strand | Q73PV9 |
| D | Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) | protein | 159 | 52% helix, 14% strand | Q73PV9 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.57 | 0.76 | 58 | EDO |
| 2 | 304 | 0.56 | 0.76 | 54 | EDO |
| 3 | 100 | 0.49 | 0.81 | 21 | EDO |
| 4 | 238 | 0.47 | 0.73 | 36 | empty |
| 5 | 98 | 0.46 | 0.80 | 20 | EDO |
Interfaces
6 interfaces between chains.
- A–D · 747 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 727 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 653 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 554 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5C5D · Crystal structure of Treponema denticola PurE2-S38D · the same entry in another collection · chain A against A, TM-score 1.00
- Q73PV9 · AlphaFold monomer V2.0 prediction for phosphoribosylaminoimidazole carboxylase (Q73PV9) · a predicted model of the same protein · chain D 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 Q73PV9
- Elsewhere: RCSB PDB 5C5D · PDBe 5C5D · UniProt Q73PV9
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