Research workbench
D-sialic acid aldolase complexed with L-arabinose
Analyse D-sialic acid aldolase complexed with L-arabinose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LBC
- Type
- protein
- Length
- 1,178 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylneuraminate lyase
- EC
- 4.1.3.3
- UniProt
- P0A6L4
- Ligands
- LAI, SO4
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 293 | 54% helix, 14% strand | P0A6L4 |
| B | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 295 | 54% helix, 13% strand | P0A6L4 |
| C | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 294 | 54% helix, 14% strand | P0A6L4 |
| D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 296 | 54% helix, 14% strand | P0A6L4 |
Ligands and binding sites
- LAI · L-arabinose · ligand · 4 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.75 | 0.90 | 31 | empty |
| 2 | 228 | 0.75 | 0.90 | 32 | empty |
| 3 | 347 | 0.69 | 0.82 | 32 | empty |
| 4 | 330 | 0.68 | 0.82 | 33 | empty |
| 5 | 348 | 0.68 | 0.82 | 31 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1237 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1235 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1057 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1056 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
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 P0A6L4
- Elsewhere: RCSB PDB 3LBC · PDBe 3LBC · UniProt P0A6L4
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