Research workbench
Structure of the E.COLI GDP-mannose hydrolase (yffh) in complex with tartrate
Analyse Structure of the E.COLI GDP-mannose hydrolase (yffh) in complex with tartrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O52
- Type
- protein
- Length
- 885 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-mannose pyrophosphatase nudk
- EC
- 3.6.1.-
- UniProt
- P37128
- Ligands
- NA, CL
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 175 | 23% helix, 45% strand | P37128 |
| B | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 176 | 23% helix, 43% strand | P37128 |
| C | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 177 | 22% helix, 44% strand | P37128 |
| D | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 180 | 21% helix, 43% strand | P37128 |
| E | GDP-mannose pyrophosphatase nudk (EC 3.6.1.-) | protein | 177 | 21% helix, 45% strand | P37128 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, D, C, E
- CL · Chloride ion · ion · 4 copies · chains C, D
- TAR · D(-)-tartaric acid · additive · 6 copies · chains A, B, C, D, E
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 | 949 | 0.87 | 0.88 | 98 | TAR, NA |
| 2 | 1067 | 0.83 | 0.84 | 106 | TAR, NA |
| 3 | 251 | 0.60 | 0.80 | 37 | TAR, NA |
| 4 | 69 | 0.38 | 0.78 | 11 | empty |
| 5 | 80 | 0.38 | 0.77 | 14 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2687 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2642 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 479 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 402 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 316 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 3O52 · Structure of the E.coli GDP-mannose hydrolase (yffh) in complex with tartrate · the same entry in another collection · chain E against E, TM-score 1.00
- P37128 · AlphaFold monomer V2.0 prediction for GDP-mannose pyrophosphatase (P37128) · a predicted model of the same protein · chain C 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 3O52 · PDBe 3O52 · UniProt P37128
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