MolNFT v1 · #80388 · protein
Crystal structure of xylose isomerase domain protein from planctomyces limnophilus
3TVA · Xylose isomerase domain protein tim barrel: “Crystal structure of xylose isomerase domain protein from planctomyces limnophilus”. X-ray diffraction, 2 ligands (MG, CL), 3 pockets (best druggability 0.69). MolNFT v1 #80388 on…
- PDB
- 3TVA
- Type
- protein
- Length
- 558 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase domain protein tim barrel
- UniProt
- D5SXE5
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylose isomerase domain protein tim barrel | protein | 282 | 45% helix, 17% strand | D5SXE5 |
| B | Xylose isomerase domain protein tim barrel | protein | 276 | 46% helix, 16% strand | D5SXE5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.69 | 0.76 | 61 | empty |
| 2 | 287 | 0.67 | 0.82 | 31 | GOL |
| 3 | 414 | 0.62 | 0.77 | 47 | GOL |
Interfaces
1 interface between chains.
- A–B · 967 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3TVA · Crystal Structure of Xylose isomerase domain protein from Planctomyces limnophilus · 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 D5SXE5
- Elsewhere: RCSB PDB 3TVA · PDBe 3TVA · UniProt D5SXE5
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