Research workbench
Complex of trypanosoma cruzi ribose 5-phosphate isomerase type B with ribose 5-phosphate
Analyse Complex of trypanosoma cruzi ribose 5-phosphate isomerase type B with ribose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K7S
- Type
- protein
- Length
- 606 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose 5-phosphate isomerase
- EC
- 5.3.1.6
- UniProt
- A1BTJ7
- Ligands
- R52
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ribose 5-phosphate isomerase (EC 5.3.1.6) | protein | 152 | 47% helix, 18% strand | A1BTJ7 |
| B, D | Ribose 5-phosphate isomerase (EC 5.3.1.6) | protein | 151 | 48% helix, 18% strand | A1BTJ7 |
Ligands and binding sites
- R52 · 5-O-phosphono-D-ribose · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.79 | 0.98 | 21 | empty |
| 2 | 62 | 0.62 | 0.92 | 18 | R52 |
| 3 | 67 | 0.58 | 0.89 | 17 | R52 |
| 4 | 53 | 0.57 | 0.91 | 16 | R52 |
| 5 | 97 | 0.54 | 0.84 | 19 | R52 |
Interfaces
6 interfaces between chains.
- C–D · 1869 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1837 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 339 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 335 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 273 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3K7S · Complex of Trypanosoma cruzi ribose 5-phosphate isomerase type B with ribose 5-phosphate · 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 A1BTJ7
- Elsewhere: RCSB PDB 3K7S · PDBe 3K7S · UniProt A1BTJ7
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