MolNFT v1 · #70164 · protein
The D-sialic acid aldolase mutant V251W
3LCI · N-acetylneuraminate lyase: “The D-sialic acid aldolase mutant V251W”. X-ray diffraction, 1 ligand (SO4), 15 pockets (best druggability 0.76). MolNFT v1 #70164 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3LCI
- 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
- SO4
- Pockets
- 15 · best druggability 0.76
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, 13% strand | P0A6L4 |
| B | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 295 | 54% helix, 14% 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
- 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
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 | 208 | 0.76 | 0.91 | 27 | empty |
| 2 | 203 | 0.75 | 0.90 | 24 | empty |
| 3 | 299 | 0.67 | 0.82 | 33 | SO4 |
| 4 | 299 | 0.67 | 0.82 | 34 | SO4 |
| 5 | 295 | 0.67 | 0.82 | 33 | SO4 |
Interfaces
4 interfaces between chains.
- A–D · 1241 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1217 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1045 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1039 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3LCI · The D-sialic acid aldolase mutant V251W · 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 3LCI · PDBe 3LCI · UniProt P0A6L4
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