Research workbench
Crystal structure of mannose 6-phosphate isomerase bound with zinc and yttrium
Analyse Crystal structure of mannose 6-phosphate isomerase bound with zinc and yttrium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H1W
- Type
- protein
- Length
- 390 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-6-phosphate isomerase
- EC
- 5.3.1.8
- UniProt
- P25081
- Ligands
- ZN, Y1
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannose-6-phosphate isomerase (EC 5.3.1.8) | protein | 390 | 29% helix, 29% strand | P25081 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- Y1 · Yttrium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.68 | 0.78 | 41 | Y1 |
| 2 | 62 | 0.37 | 0.79 | 19 | empty |
| 3 | 53 | 0.35 | 0.79 | 13 | empty |
| 4 | 67 | 0.34 | 0.77 | 16 | EDO |
Compared structures
- 3H1W · Crystal structure of mannose 6-phosphate isomerase bound with zinc and yttrium · the same entry in another collection · chain A against A, TM-score 1.00
- P25081 · AlphaFold monomer V2.0 prediction for mannose-6-phosphate isomerase (P25081) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P25081
- Elsewhere: RCSB PDB 3H1W · PDBe 3H1W · UniProt P25081
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