Research workbench
Structure of the D152A E.COLI GDP-mannose hydrolase (yffh) in complex with mg++
Analyse Structure of the D152A 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
- 3O6Z
- Type
- protein
- Length
- 369 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, CL
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 181 | 22% helix, 43% strand | P37128 |
| B | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 188 | 23% helix, 41% strand | P37128 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.69 | 0.81 | 50 | MG |
| 2 | 289 | 0.62 | 0.80 | 40 | MG |
| 3 | 86 | 0.39 | 0.77 | 12 | empty |
| 4 | 66 | 0.35 | 0.77 | 12 | empty |
| 5 | 84 | 0.35 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2728 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3O6Z · Structure of the D152A 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 3O6Z · PDBe 3O6Z · UniProt P37128
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