Research workbench
1.85 ångström resolution crystal structure of fructose-bisphosphate aldolase (fba) from campylobacter jejuni
Analyse 1.85 ångström resolution crystal structure of fructose-bisphosphate aldolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QM3
- Type
- protein
- Length
- 2,764 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fructose-bisphosphate aldolase
- EC
- 4.1.2.13
- UniProt
- Q0PAS0
- Ligands
- ZN, SO4, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 350 | 51% helix, 13% strand | Q0PAS0 |
| B | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 344 | 52% helix, 14% strand | Q0PAS0 |
| C | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 344 | 52% helix, 14% strand | Q0PAS0 |
| D | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 344 | 53% helix, 14% strand | Q0PAS0 |
| F | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 343 | 52% helix, 14% strand | Q0PAS0 |
| H | Fructose-bisphosphate aldolase (EC 4.1.2.13) | protein | 339 | 53% helix, 14% strand | Q0PAS0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · chains D
- FMT · Formic acid · additive · 5 copies · chains A, D, C, F, H
- GOL · Glycerol · additive · 5 copies · chains B, C, E, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.77 | 0.79 | 103 | empty |
| 2 | 802 | 0.75 | 0.79 | 83 | empty |
| 3 | 739 | 0.70 | 0.77 | 81 | GOL |
| 4 | 602 | 0.65 | 0.76 | 57 | SO4 |
| 5 | 566 | 0.65 | 0.76 | 57 | SO4 |
Interfaces
14 interfaces between chains.
- A–B · 2498 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2474 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2447 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2446 Ų buried · 23 hydrogen bonds · protein-protein
- A–G · 445 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3QM3 · 1.85 Angstrom Resolution Crystal Structure of Fructose-bisphosphate Aldolase (Fba) from… · the same entry in another collection · chain H against H, TM-score 1.00
- Q0PAS0 · AlphaFold monomer V2.0 prediction for fructose-bisphosphate aldolase (Q0PAS0) · a predicted model of the same protein · chain H against A, TM-score 0.97
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 Q0PAS0
- Elsewhere: RCSB PDB 3QM3 · PDBe 3QM3 · UniProt Q0PAS0
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