MolNFT v1 · #49089 · protein
Fructose-1,6-bisphosphate aldolase from leishmania mexicana in complex with mannitol-1,6-bisphosphate, a competitive inhibitor
2QDH: “Fructose-1,6-bisphosphate aldolase from leishmania mexicana in complex with mannitol-1,6-bisphosphate, a…”. X-ray diffraction, 1 ligand (M2P), 15 pockets (best druggability 0.88). MolNFT v1 #49089 on GenesisL1: 3D structure, binding…
- PDB
- 2QDH
- Type
- protein
- Length
- 1,448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-1,6-bisphosphate aldolase
- EC
- 4.1.2.13
- UniProt
- Q9U5N6
- Ligands
- M2P
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) | protein | 366 | 44% helix, 16% strand | Q9U5N6 |
| C, D | Fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) | protein | 358 | 48% helix, 17% strand | Q9U5N6 |
Ligands and binding sites
- M2P · D-mannitol-1,6-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.88 | 0.89 | 136 | empty |
| 2 | 198 | 0.75 | 0.90 | 39 | empty |
| 3 | 428 | 0.68 | 0.80 | 46 | M2P |
| 4 | 411 | 0.67 | 0.80 | 43 | M2P |
| 5 | 251 | 0.62 | 0.81 | 29 | M2P |
Interfaces
6 interfaces between chains.
- B–C · 1548 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1546 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1519 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1501 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 638 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2QDH · Fructose-1,6-bisphosphate aldolase from Leishmania mexicana in complex with… · the same entry in another collection · chain A 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 Q9U5N6
- Elsewhere: RCSB PDB 2QDH · PDBe 2QDH · UniProt Q9U5N6
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