Research workbench
Crystal structure of human liver fbpase complexed with an covalent inhibitor
Analyse Crystal structure of human liver fbpase complexed with an covalent inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WJV
- Type
- protein
- Length
- 1,295 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-1,6-bisphosphatase 1
- UniProt
- Q2TU34
- Ligands
- AMP, LSA, PMQ, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructose-1,6-bisphosphatase 1 | protein | 322 | 38% helix, 24% strand | Q2TU34 |
| B | Fructose-1,6-bisphosphatase 1 | protein | 327 | 37% helix, 24% strand | Q2TU34 |
| C | Fructose-1,6-bisphosphatase 1 | protein | 326 | 37% helix, 25% strand | Q2TU34 |
| D | Fructose-1,6-bisphosphatase 1 | protein | 320 | 38% helix, 24% strand | Q2TU34 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- LSA · 1,2-benzisothiazol-3(2H)-one 1,1-dioxide · ligand · chains A, B
- PMQ · benzylcarbamic acid · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.87 | 0.88 | 116 | empty |
| 2 | 272 | 0.65 | 0.82 | 53 | empty |
| 3 | 244 | 0.63 | 0.81 | 31 | PMQ |
| 4 | 79 | 0.53 | 0.85 | 19 | empty |
| 5 | 207 | 0.52 | 0.77 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2414 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2284 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1265 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1252 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 508 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7WJV · Crystal structure of human liver FBPase complexed with an covalent inhibitor · the same entry in another collection · chain A 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 Q2TU34
- Elsewhere: RCSB PDB 7WJV · PDBe 7WJV · UniProt Q2TU34
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