Research workbench
Crystal structure of L-xylulose-5-phosphate 3-epimerase ulae (form B) complex with ZN2+
Analyse Crystal structure of L-xylulose-5-phosphate 3-epimerase ulae (form B) complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CQJ
- Type
- protein
- Length
- 551 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-ribulose-5-phosphate 3-epimerase ulae
- EC
- 5.1.3.22
- UniProt
- Q8XDI5
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-ribulose-5-phosphate 3-epimerase ulae (EC 5.1.3.22) | protein | 276 | 51% helix, 16% strand | Q8XDI5 |
| B | L-ribulose-5-phosphate 3-epimerase ulae (EC 5.1.3.22) | protein | 275 | 52% helix, 16% strand | Q8XDI5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 224 | 0.59 | 0.80 | 32 | empty |
| 2 | 111 | 0.56 | 0.84 | 25 | empty |
| 3 | 121 | 0.54 | 0.83 | 25 | empty |
| 4 | 175 | 0.53 | 0.79 | 16 | empty |
| 5 | 74 | 0.47 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1727 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3CQJ · Crystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE (form B) complex with Zn2+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q8XDI5 · AlphaFold monomer V2.0 prediction for L-ribulose-5-phosphate 3-epimerase ulae (Q8XDI5) · a predicted model of the same protein · 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 Q8XDI5
- Elsewhere: RCSB PDB 3CQJ · PDBe 3CQJ · UniProt Q8XDI5
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