MolNFT v1 · #70167 · protein
The D-sialic acid aldolase mutant V251I/V265I
3LCL · N-acetylneuraminate lyase: “The D-sialic acid aldolase mutant V251I/V265I”. X-ray diffraction, 1 ligand (SO4), 13 pockets (best druggability 0.76). MolNFT v1 #70167 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3LCL
- 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
- 13 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 293 | 55% helix, 13% 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, 13% 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
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.76 | 0.91 | 27 | empty |
| 2 | 205 | 0.75 | 0.90 | 27 | empty |
| 3 | 297 | 0.69 | 0.83 | 34 | SO4 |
| 4 | 291 | 0.68 | 0.83 | 31 | empty |
| 5 | 290 | 0.68 | 0.83 | 38 | SO4 |
Interfaces
4 interfaces between chains.
- B–C · 1238 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1231 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1053 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1050 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3LCL · The D-sialic acid aldolase mutant V251I/V265I · 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 3LCL · PDBe 3LCL · UniProt P0A6L4
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