MolNFT v1 · #55330 · protein
Structure of wild type E. COLI N-acetylneuraminic acid lyase in space group P21 crystal form II
2YGY · N-acetylneuraminate lyase: “Structure of wild type E. COLI N-acetylneuraminic acid lyase in space group P21 crystal form II”. X-ray diffraction, 1 ligand (CL), 14 pockets (best druggability 0.78). MolNFT v1 #55330 on GenesisL1: 3D…
- PDB
- 2YGY
- Type
- protein
- Length
- 1,189 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
- CL
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 299 | 55% helix, 13% strand | P0A6L4 |
| B | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 295 | 55% helix, 13% strand | P0A6L4 |
| C | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 296 | 53% helix, 12% strand | P0A6L4 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.78 | 0.80 | 82 | CL |
| 2 | 195 | 0.74 | 0.90 | 26 | empty |
| 3 | 197 | 0.74 | 0.90 | 26 | empty |
| 4 | 346 | 0.71 | 0.83 | 32 | empty |
| 5 | 316 | 0.68 | 0.82 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1250 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1142 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1070 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1069 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2YGY · Structure of wild type E. coli N-acetylneuraminic acid lyase in space group P21 crystal… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6L4 · AlphaFold monomer V2.0 prediction for N-acetylneuraminate lyase (P0A6L4) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 2YGY · PDBe 2YGY · UniProt P0A6L4
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