Research workbench
Structure of the E100A E.COLI GDP-mannose hydrolase (yffh) in complex with GDP-mannose and mg++
Analyse Structure of the E100A E.COLI GDP-mannose hydrolase (yffh) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O61
- Type
- protein
- Length
- 746 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-mannose pyrophosphatase nudk
- EC
- 3.6.1.-
- UniProt
- P37128
- Ligands
- GDD, MG, NA, CL
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 187 | 22% helix, 43% strand | P37128 |
| B | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 187 | 23% helix, 42% strand | P37128 |
| C | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 182 | 22% helix, 43% strand | P37128 |
| D | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 190 | 20% helix, 43% strand | P37128 |
Ligands and binding sites
- GDD · Guanosine-5'-diphosphate-alpha-D-mannose · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.72 | 0.83 | 49 | GDD, MG |
| 2 | 301 | 0.67 | 0.82 | 40 | GDD, MG |
| 3 | 284 | 0.66 | 0.82 | 41 | GDD, MG |
| 4 | 324 | 0.66 | 0.81 | 44 | GDD, MG |
| 5 | 325 | 0.63 | 0.79 | 37 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2907 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2775 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 480 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 253 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3O61 · Structure of the E100A E.coli GDP-mannose hydrolase (yffh) in complex with GDP-mannose… · the same entry in another collection · chain D against D, 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 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 P37128
- Elsewhere: RCSB PDB 3O61 · PDBe 3O61 · UniProt P37128
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