Research workbench
Crystal structure of ribulose-phosphate 3-epimerase from pseudomonas aeruginosa
Analyse Crystal structure of ribulose-phosphate 3-epimerase from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U5Y
- Type
- protein
- Length
- 1,336 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
- Q9I5T1
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 227 | 40% helix, 19% strand | Q9I5T1 |
| B | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 222 | 42% helix, 20% strand | Q9I5T1 |
| C | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 220 | 43% helix, 20% strand | Q9I5T1 |
| D, E | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 223 | 43% helix, 18% strand | Q9I5T1 |
| F | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 221 | 39% helix, 19% strand | Q9I5T1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.80 | 0.84 | 49 | empty |
| 2 | 791 | 0.79 | 0.83 | 57 | empty |
| 3 | 318 | 0.60 | 0.78 | 34 | empty |
| 4 | 310 | 0.59 | 0.78 | 36 | empty |
| 5 | 289 | 0.59 | 0.78 | 35 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1155 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1140 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 1140 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 633 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 630 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7U5Y · Crystal structure of ribulose-phosphate 3-epimerase from Pseudomonas aeruginosa · 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 Q9I5T1
- Elsewhere: RCSB PDB 7U5Y · PDBe 7U5Y · UniProt Q9I5T1
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