Research workbench
Class II fructose-1,6-bisphosphate aldolase from thermus aquaticus in complex with cobalt
Analyse Class II fructose-1,6-bisphosphate aldolase from thermus aquaticus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RV8
- Type
- protein
- Length
- 1,212 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
- Q9RHA2
- Ligands
- CO, NA, SO4
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) | protein | 297 | 51% helix, 15% strand | Q9RHA2 |
| B, C, D | Fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) | protein | 305 | 50% helix, 14% strand | Q9RHA2 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 5 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.68 | 0.81 | 46 | empty |
| 2 | 266 | 0.51 | 0.74 | 31 | SO4 |
| 3 | 216 | 0.47 | 0.74 | 26 | SO4 |
| 4 | 222 | 0.47 | 0.74 | 26 | SO4 |
| 5 | 102 | 0.44 | 0.79 | 22 | SO4 |
Interfaces
3 interfaces between chains.
- C–D · 1915 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1907 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 513 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1RV8 · Class II fructose-1,6-bisphosphate aldolase from Thermus aquaticus in complex with cobalt · the same entry in another collection · chain B against B, 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 Q9RHA2
- Elsewhere: RCSB PDB 1RV8 · PDBe 1RV8 · UniProt Q9RHA2
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