Research workbench
Crystal structure of the Y103F mutant of the GDP-mannose mannosyl hydrolase in complex with GDP-mannose and MG+2
Analyse Crystal structure of the Y103F mutant of the GDP-mannose mannosyl hydrolase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GT4
- Type
- protein
- Length
- 480 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-mannose mannosyl hydrolase
- EC
- 3.6.1.-
- UniProt
- P32056
- Ligands
- GDD, BMA, MG
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | GDP-mannose mannosyl hydrolase (EC 3.6.1.-) | protein | 160 | 33% helix, 31% strand | P32056 |
Ligands and binding sites
- GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · 3 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.77 | 0.82 | 48 | BMA, MG, GDD |
| 2 | 367 | 0.67 | 0.80 | 40 | MG, GDD |
| 3 | 378 | 0.63 | 0.78 | 35 | BMA, MG, GDD |
| 4 | 91 | 0.43 | 0.79 | 23 | empty |
| 5 | 53 | 0.35 | 0.78 | 11 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1369 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 794 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 2GT4 · Crystal Structure of the Y103F mutant of the GDP-mannose mannosyl hydrolase in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P32056 · AlphaFold monomer V2.0 prediction for GDP-mannose mannosyl hydrolase (P32056) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P32056
- Elsewhere: RCSB PDB 2GT4 · PDBe 2GT4 · UniProt P32056
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