Research workbench
Crystal structure of D-allulose 6-phosphate 3-epimerase from escherichia COLI K12 complexed with D-glucitol 6- phosphate and magnesium
Analyse Crystal structure of D-allulose 6-phosphate 3-epimerase from escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CTL
- Type
- protein
- Length
- 1,314 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-allulose-6-phosphate 3-epimerase
- EC
- 5.1.3.-
- UniProt
- P32719
- Ligands
- S6P, MG
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | D-allulose-6-phosphate 3-epimerase (EC 5.1.3.-) | protein | 219 | 42% helix, 19% strand | P32719 |
Ligands and binding sites
- S6P · D-sorbitol-6-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium 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
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.76 | 0.82 | 56 | empty |
| 2 | 694 | 0.76 | 0.81 | 59 | empty |
| 3 | 97 | 0.71 | 0.94 | 28 | S6P |
| 4 | 88 | 0.70 | 0.94 | 27 | S6P |
| 5 | 89 | 0.70 | 0.94 | 26 | S6P |
Interfaces
12 interfaces between chains.
- D–F · 1168 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1165 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1157 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 614 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 604 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3CTL · Crystal structure of D-Allulose 6-Phosphate 3-Epimerase from Escherichia coli K12… · the same entry in another collection · chain F against F, TM-score 1.00
- P32719 · AlphaFold monomer V2.0 prediction for D-allulose-6-phosphate 3-epimerase (P32719) · a predicted model of the same protein · chain B 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 P32719
- Elsewhere: RCSB PDB 3CTL · PDBe 3CTL · UniProt P32719
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