MolNFT v1 · #101529 · protein
2.05 ångström crystal structure of ribulose-phosphate 3-epimerase from toxoplasma gondii.
4NU7: “2.05 ångström crystal structure of ribulose-phosphate 3-epimerase from toxoplasma gondii.”. X-ray diffraction, 3 ligands (ZN, SO4, CL), 5 pockets (best druggability 0.79). MolNFT v1 #101529 on GenesisL1: 3D structure, binding sites…
- PDB
- 4NU7
- Type
- protein
- Length
- 903 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-phosphate 3-epimerase
- EC
- 5.1.3.1
- UniProt
- B9PPN9
- Ligands
- ZN, SO4, CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 225 | 44% helix, 21% strand | B9PPN9 |
| C | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 227 | 44% helix, 21% strand | B9PPN9 |
| D | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 226 | 43% helix, 21% strand | B9PPN9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, D, C
- CL · Chloride ion · ion · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.79 | 0.86 | 75 | CL, SO4 |
| 2 | 358 | 0.70 | 0.83 | 42 | SO4 |
| 3 | 94 | 0.63 | 0.89 | 25 | SO4 |
| 4 | 206 | 0.60 | 0.81 | 44 | SO4 |
| 5 | 206 | 0.59 | 0.81 | 43 | SO4 |
Interfaces
5 interfaces between chains.
- B–D · 965 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 956 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 321 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 319 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 98 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4NU7 · 2.05 Angstrom Crystal Structure of Ribulose-phosphate 3-epimerase from Toxoplasma gondii. · 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 B9PPN9
- Elsewhere: RCSB PDB 4NU7 · PDBe 4NU7 · UniProt B9PPN9
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