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Crystal structure of ribulose-phosphate 3-epimerase from stenotrophomonas maltophilia K279A
Analyse Crystal structure of ribulose-phosphate 3-epimerase from stenotrophomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SBJ
- Type
- protein
- Length
- 663 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
- B2FKL8
- Ligands
- ZN, MG, CL, SO4
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | protein | 221 | 44% helix, 19% strand | B2FKL8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · 9 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 6 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.60 | 0.80 | 35 | SO4, CL |
| 2 | 211 | 0.60 | 0.81 | 29 | SO4, CL |
| 3 | 157 | 0.57 | 0.82 | 26 | SO4, CL |
| 4 | 182 | 0.51 | 0.77 | 26 | CL |
| 5 | 81 | 0.35 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1220 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 662 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7SBJ · Crystal Structure of Ribulose-phosphate 3-epimerase from Stenotrophomonas maltophilia… · 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 B2FKL8
- Elsewhere: RCSB PDB 7SBJ · PDBe 7SBJ · UniProt B2FKL8
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