MolNFT v1 · #135004 · protein
Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor 1-phosphate-benzene 4-bisphosphonate
5TLW · Fructose-bisphosphate aldolase a: “Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor 1-phosphate-benzene…”. X-ray diffraction, 1 ligand (RD3), 19 pockets (best druggability 0.88). MolNFT v1 #135004…
- PDB
- 5TLW
- Type
- protein
- Length
- 1,394 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-bisphosphate aldolase a
- EC
- 4.1.2.13
- UniProt
- P00883
- Ligands
- RD3
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Fructose-bisphosphate aldolase a (EC 4.1.2.13) | protein | 349 | 46% helix, 15% strand | P00883 |
| D | Fructose-bisphosphate aldolase a (EC 4.1.2.13) | protein | 347 | 46% helix, 16% strand | P00883 |
Ligands and binding sites
- RD3 · {[4-(phosphonooxy)phenyl]methylene}bis(phosphonic acid) · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.88 | 0.89 | 116 | empty |
| 2 | 579 | 0.84 | 0.89 | 72 | empty |
| 3 | 305 | 0.77 | 0.88 | 48 | empty |
| 4 | 231 | 0.73 | 0.88 | 30 | empty |
| 5 | 176 | 0.66 | 0.86 | 47 | GOL |
Interfaces
6 interfaces between chains.
- B–C · 1679 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1662 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1216 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1212 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 113 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5TLW · Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor… · the same entry in another collection · chain D against D, TM-score 1.00
- P00883 · AlphaFold monomer V2.0 prediction for fructose-bisphosphate aldolase a (P00883) · a predicted model of the same protein · chain D 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 P00883
- Elsewhere: RCSB PDB 5TLW · PDBe 5TLW · UniProt P00883
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