Research workbench
Crystal structure of a putative xylose isomerase (YP_426450.1) from rhodospirillum rubrum atcc 11170 at 1.90 a resolution
Analyse Crystal structure of a putative xylose isomerase (YP_426450.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QXB
- Type
- protein
- Length
- 1,185 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative xylose isomerase
- UniProt
- Q2RUN2
- Ligands
- FE, MN, CL
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative xylose isomerase | protein | 297 | 48% helix, 15% strand | Q2RUN2 |
| B, C, D | Putative xylose isomerase | protein | 296 | 49% helix, 15% strand | Q2RUN2 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.82 | 0.83 | 101 | EDO |
| 2 | 779 | 0.82 | 0.85 | 71 | MN, FE, EDO |
| 3 | 220 | 0.60 | 0.81 | 29 | empty |
| 4 | 315 | 0.52 | 0.74 | 42 | EDO |
| 5 | 159 | 0.42 | 0.74 | 31 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 2152 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2104 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 189 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 61 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 3QXB · Crystal structure of a Putative Xylose isomerase (YP_426450.1) from RHODOSPIRILLUM RUBRUM… · 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 Q2RUN2
- Elsewhere: RCSB PDB 3QXB · PDBe 3QXB · UniProt Q2RUN2
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