MolNFT v1 · #53266 · protein
Crystal structure of the E192N mutant of E. COLI N- acetylneuraminic acid lyase in complex with pyruvate and the inhibitor (2R,3R)-2,3,4-trihydroxy-N,N- dipropylbutanamide in space group P21 crystal form I
2WPB · N-acetylneuraminate lyase: “Crystal structure of the E192N mutant of E. COLI N- acetylneuraminic acid lyase in complex with pyruvate and…”. X-ray diffraction, 1 ligand (ZZI), 13 pockets (best druggability 0.75). MolNFT v1 #53266 on…
- PDB
- 2WPB
- Type
- protein
- Length
- 1,187 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
- ZZI
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 302 | 54% helix, 13% strand | P0A6L4 |
| B, C, D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 295 | 55% helix, 13% strand | P0A6L4 |
Ligands and binding sites
- ZZI · (2R,3R)-2,3,4-trihydroxy-N,N-dipropylbutanamide · ligand · 4 copies · chains A, C, B, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.75 | 0.90 | 27 | empty |
| 2 | 195 | 0.73 | 0.89 | 27 | empty |
| 3 | 331 | 0.68 | 0.82 | 31 | ZZI |
| 4 | 321 | 0.68 | 0.82 | 34 | ZZI |
| 5 | 417 | 0.67 | 0.79 | 44 | ZZI |
Interfaces
4 interfaces between chains.
- B–C · 1246 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1245 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1068 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1052 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 2WPB · Crystal structure of the E192N mutant of E. Coli N-acetylneuraminic acid lyase in complex… · 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 B 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 2WPB · PDBe 2WPB · UniProt P0A6L4
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