MolNFT v1 · #125610 · protein
Quadruple space group ambiguity due to rotational and translational non-crystallographic symmetry in human liver fructose-1,6- bisphosphatase
5LDZ · Fructose-1,6-bisphosphatase 1: “Quadruple space group ambiguity due to rotational and translational non-crystallographic symmetry in human…”. X-ray diffraction, 3 ligands (ZN, SO4, CL), 20 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 5LDZ
- Type
- protein
- Length
- 1,872 residues
- Chains
- 6
- 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
- ZN, SO4, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 311 | 39% helix, 24% strand | P09467 |
| B | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 312 | 38% helix, 24% strand | P09467 |
| C | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 311 | 38% helix, 24% strand | P09467 |
| D | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 313 | 39% helix, 25% strand | P09467 |
| F | Fructose-1,6-bisphosphatase 1 (EC 3.1.3.11) | protein | 314 | 38% helix, 24% strand | P09467 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 29 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 3 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.83 | 0.84 | 107 | empty |
| 2 | 657 | 0.71 | 0.78 | 66 | empty |
| 3 | 839 | 0.70 | 0.76 | 92 | SO4 |
| 4 | 68 | 0.62 | 0.91 | 25 | empty |
| 5 | 84 | 0.59 | 0.88 | 30 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2218 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2215 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2190 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1487 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1481 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5LDZ · Quadruple space group ambiguity due to rotational and translational non-crystallographic… · the same entry in another collection · chain F against F, 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 F 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 P09467
- Elsewhere: RCSB PDB 5LDZ · PDBe 5LDZ · UniProt P09467
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