Research workbench
Crystal structure analysis of the mannose 6-phosphate isomerase from bacillus subtilis
Analyse Crystal structure analysis of the mannose 6-phosphate isomerase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QWR
- Type
- protein
- Length
- 629 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-6-phosphate isomerase
- EC
- 5.3.1.8
- UniProt
- P39841
- Ligands
- ZN, SO4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannose-6-phosphate isomerase (EC 5.3.1.8) | protein | 315 | 14% helix, 43% strand | P39841 |
| B | Mannose-6-phosphate isomerase (EC 5.3.1.8) | protein | 314 | 13% helix, 44% strand | P39841 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.74 | 0.78 | 73 | empty |
| 2 | 198 | 0.60 | 0.82 | 32 | SO4, ZN |
| 3 | 166 | 0.58 | 0.82 | 31 | SO4, ZN |
| 4 | 91 | 0.41 | 0.77 | 14 | empty |
| 5 | 99 | 0.40 | 0.76 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 531 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1QWR · Crystal Structure Analysis of the Mannose 6-Phosphate Isomerase from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P39841 · AlphaFold monomer V2.0 prediction for putative mannose-6-phosphate isomerase yvyi (P39841) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P39841
- Elsewhere: RCSB PDB 1QWR · PDBe 1QWR · UniProt P39841
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