Research workbench
Crystal structure of human liver fbpase in complex with tricyclic inhibitor 6
Analyse Crystal structure of human liver fbpase in complex with tricyclic inhibitor 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KBZ
- Type
- protein
- Length
- 1,273 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-1,6-bisphosphatase 1
- EC
- 3.1.3.11
- UniProt
- P09467
- Ligands
- 2T4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 319 | 39% helix, 24% strand | P09467 |
| B, C, D | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 318 | 38% helix, 25% strand | P09467 |
Ligands and binding sites
- 2T4 · {[(2-amino-8H-indeno[1,2-d][1,3]thiazol-4-yl)oxy]methyl}phosphonic acid · ligand · 4 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.82 | 0.83 | 111 | empty |
| 2 | 540 | 0.65 | 0.76 | 67 | empty |
| 3 | 135 | 0.54 | 0.82 | 39 | empty |
| 4 | 196 | 0.54 | 0.79 | 30 | empty |
| 5 | 161 | 0.50 | 0.78 | 27 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2418 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2375 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1241 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1093 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 444 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3KBZ · Crystal structure of human liver FBPase in complex with tricyclic inhibitor 6 · the same entry in another collection · chain D against D, TM-score 1.00
- P09467 · AlphaFold monomer V2.0 prediction for fructose-1,6-bisphosphatase 1 (P09467) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P09467
- Elsewhere: RCSB PDB 3KBZ · PDBe 3KBZ · UniProt P09467
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