Research workbench
Single particle reconstruction of glucose isomerase from streptomyces rubiginosus based on data acquired in the presence of substantial aberrations
Analyse Single particle reconstruction of glucose isomerase from streptomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VRS
- Type
- protein
- Length
- 1,548 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P24300
- Ligands
- MN
- Pockets
- 19 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Xylose isomerase (EC 5.3.1.5) | protein | 387 | 49% helix, 10% strand | P24300 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.85 | 0.91 | 88 | empty |
| 2 | 608 | 0.85 | 0.90 | 100 | empty |
| 3 | 235 | 0.82 | 0.95 | 42 | empty |
| 4 | 116 | 0.76 | 0.95 | 24 | empty |
| 5 | 112 | 0.75 | 0.95 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–C · 4888 Ų buried · 70 hydrogen bonds · protein-protein
- A–D · 4885 Ų buried · 70 hydrogen bonds · protein-protein
- A–C · 1635 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 1624 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1598 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6VRS · Single particle reconstruction of glucose isomerase from Streptomyces rubiginosus based… · 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 P24300
- Elsewhere: RCSB PDB 6VRS · PDBe 6VRS · UniProt P24300
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