MolNFT v1 · #55179 · protein
Structure of an archaeal fructose-1,6-bisphosphate aldolase with the catalytic lys covalently bound to the carbinolamine intermediate of the substrate.
2YCE · Fructose-bisphosphate aldolase class 1: “Structure of an archaeal fructose-1,6-bisphosphate aldolase with the catalytic lys covalently bound to the…”. X-ray diffraction, 1 ligand (M2P), 20 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 2YCE
- Type
- protein
- Length
- 2,506 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-bisphosphate aldolase class 1
- EC
- 4.1.2.13
- UniProt
- P58315
- Ligands
- M2P
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F, G, H, I, J | Fructose-bisphosphate aldolase class 1 (EC 4.1.2.13) | protein | 250 | 46% helix, 16% strand | P58315 |
| B | Fructose-bisphosphate aldolase class 1 (EC 4.1.2.13) | protein | 251 | 46% helix, 16% strand | P58315 |
| E | Fructose-bisphosphate aldolase class 1 (EC 4.1.2.13) | protein | 255 | 46% helix, 16% strand | P58315 |
Ligands and binding sites
- M2P · D-mannitol-1,6-diphosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.72 | 0.78 | 62 | empty |
| 2 | 710 | 0.72 | 0.78 | 57 | empty |
| 3 | 483 | 0.66 | 0.78 | 38 | empty |
| 4 | 636 | 0.66 | 0.76 | 42 | empty |
| 5 | 625 | 0.66 | 0.75 | 66 | empty |
Interfaces
15 interfaces between chains.
- I–J · 1564 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1557 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1547 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1545 Ų buried · 20 hydrogen bonds · protein-protein
- H–I · 1544 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent (covalent ligand).
Compared structures
- 2YCE · Structure of an Archaeal fructose-1,6-bisphosphate aldolase with the catalytic Lys… · the same entry in another collection · chain J against J, TM-score 1.00
- P58315 · AlphaFold monomer V2.0 prediction for fructose-bisphosphate aldolase class 1 (P58315) · a predicted model of the same protein · chain E 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 P58315
- Elsewhere: RCSB PDB 2YCE · PDBe 2YCE · UniProt P58315
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