Research workbench
Structure of the E100A E.COLI GDP-mannose hydrolase (yffh) in complex with mg++
Analyse Structure of the E100A E.COLI GDP-mannose hydrolase (yffh) in complex with mg++ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O69
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-mannose pyrophosphatase nudk
- EC
- 3.6.1.-
- UniProt
- P37128
- Ligands
- MG, NA, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 176 | 22% helix, 44% strand | P37128 |
| B | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 189 | 22% helix, 42% strand | P37128 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.70 | 0.81 | 51 | NA, MG |
| 2 | 283 | 0.62 | 0.80 | 42 | MG |
| 3 | 77 | 0.37 | 0.77 | 15 | empty |
| 4 | 73 | 0.35 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2824 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3O69 · Structure of the E100A E.coli GDP-mannose hydrolase (yffh) in complex with Mg++ · the same entry in another collection · chain A against A, TM-score 1.00
- P37128 · AlphaFold monomer V2.0 prediction for GDP-mannose pyrophosphatase (P37128) · a predicted model of the same protein · chain B 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 P37128
- Elsewhere: RCSB PDB 3O69 · PDBe 3O69 · UniProt P37128
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.