Research workbench
Crystal structure of D-ribulose 5-phosphate 3-epimerase from synechocystis to 1.6 ångström resolution
Analyse Crystal structure of D-ribulose 5-phosphate 3-epimerase from synechocystis to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TQJ
- Type
- protein
- Length
- 1,297 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-phosphate 3-epimerase
- EC
- 5.1.3.1
- UniProt
- P74061
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 217 | 41% helix, 22% strand | P74061 |
| B | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 214 | 42% helix, 22% strand | P74061 |
| C | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 218 | 40% helix, 22% strand | P74061 |
| D | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 216 | 40% helix, 22% strand | P74061 |
| E | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 215 | 41% helix, 22% strand | P74061 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.81 | 0.83 | 91 | empty |
| 2 | 207 | 0.53 | 0.77 | 30 | empty |
| 3 | 90 | 0.52 | 0.84 | 28 | empty |
| 4 | 156 | 0.51 | 0.79 | 32 | empty |
| 5 | 136 | 0.43 | 0.76 | 21 | empty |
Interfaces
12 interfaces between chains.
- A–F · 1050 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1050 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 1018 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 741 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 725 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1TQJ · Crystal structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6… · the same entry in another collection · chain F against F, TM-score 1.00
- P74061 · AlphaFold monomer V2.0 prediction for ribulose-phosphate 3-epimerase (P74061) · a predicted model of the same protein · chain D 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 P74061
- Elsewhere: RCSB PDB 1TQJ · PDBe 1TQJ · UniProt P74061
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