Research workbench
Crystal structure of a ribulose-phosphate 3-epimerase from neisseria gonorrhoeae with bound phosphate
Analyse Crystal structure of a ribulose-phosphate 3-epimerase from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UMF
- Type
- protein
- Length
- 670 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-phosphate 3-epimerase
- EC
- 5.1.3.1
- UniProt
- B4RLV9
- Ligands
- ZN, PO4
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 223 | 46% helix, 19% strand | B4RLV9 |
| C | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 224 | 45% helix, 20% strand | B4RLV9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.67 | 0.95 | 25 | PO4 |
| 2 | 53 | 0.64 | 0.95 | 25 | PO4 |
| 3 | 55 | 0.62 | 0.93 | 24 | PO4 |
| 4 | 195 | 0.49 | 0.76 | 23 | empty |
| 5 | 95 | 0.40 | 0.77 | 19 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1012 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 657 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5UMF · Crystal Structure of a Ribulose-phosphate 3-epimerase from Neisseria gonorrhoeae with… · 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 B4RLV9
- Elsewhere: RCSB PDB 5UMF · PDBe 5UMF · UniProt B4RLV9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.