Research workbench
Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the inhibitor 2-naphthol 6-bisphosphonate
Analyse Fructose-1,6-bisphosphate aldolase from rabbit muscle in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TLH
- 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
- RD2, MDN
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructose-bisphosphate aldolase a (EC 4.1.2.13) | protein | 350 | 45% helix, 15% strand | P00883 |
| B | Fructose-bisphosphate aldolase a (EC 4.1.2.13) | protein | 349 | 46% helix, 15% strand | P00883 |
| C | Fructose-bisphosphate aldolase a (EC 4.1.2.13) | protein | 351 | 46% helix, 15% strand | P00883 |
| D | Fructose-bisphosphate aldolase a (EC 4.1.2.13) | protein | 344 | 46% helix, 16% strand | P00883 |
Ligands and binding sites
- RD2 · [(6-hydroxynaphthalen-2-yl)methylene]bis(phosphonic acid) · ligand · 4 copies · chains A, B, C, D
- MDN · Methylenediphosphonic 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
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.88 | 0.89 | 117 | empty |
| 2 | 555 | 0.83 | 0.89 | 75 | empty |
| 3 | 681 | 0.80 | 0.84 | 100 | empty |
| 4 | 164 | 0.66 | 0.87 | 45 | GOL |
| 5 | 372 | 0.64 | 0.79 | 38 | RD2, MDN |
Interfaces
6 interfaces between chains.
- B–C · 1683 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1507 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1237 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1224 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 99 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5TLH · 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 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 P00883
- Elsewhere: RCSB PDB 5TLH · PDBe 5TLH · UniProt P00883
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