Research workbench
L-kdo aldolase complexed with hydroxypyruvate
Analyse L-kdo aldolase complexed with hydroxypyruvate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LCW
- Type
- protein
- Length
- 1,164 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
- 3PY, SO4
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 291 | 53% helix, 13% strand | P0A6L4 |
Ligands and binding sites
- 3PY · 3-hydroxypyruvic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.75 | 0.90 | 28 | empty |
| 2 | 194 | 0.74 | 0.90 | 28 | empty |
| 3 | 476 | 0.68 | 0.79 | 63 | empty |
| 4 | 411 | 0.67 | 0.80 | 56 | 3PY |
| 5 | 293 | 0.67 | 0.82 | 34 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1226 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1226 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1085 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1040 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3LCW · L-KDO aldolase complexed with hydroxypyruvate · 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 P0A6L4
- Elsewhere: RCSB PDB 3LCW · PDBe 3LCW · UniProt P0A6L4
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