MolNFT v1 · #53099 · protein
Crystal structure of the E192N mutant of E. COLI N-acetylneuraminic acid lyase in complex with pyruvate at 1.45A resolution in space group P212121
2WKJ · N-acetylneuraminate lyase: “Crystal structure of the E192N mutant of E. COLI N-acetylneuraminic acid lyase in complex with pyruvate at…”. X-ray diffraction, 1 ligand (PYR), 11 pockets (best druggability 0.75). MolNFT v1 #53099 on…
- PDB
- 2WKJ
- Type
- protein
- Length
- 1,192 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
- PYR
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 298 | 55% helix, 13% strand | P0A6L4 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains C, D
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.75 | 0.91 | 26 | empty |
| 2 | 728 | 0.75 | 0.80 | 73 | PYR |
| 3 | 193 | 0.74 | 0.90 | 26 | empty |
| 4 | 369 | 0.68 | 0.81 | 36 | PYR |
| 5 | 342 | 0.67 | 0.81 | 36 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1243 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1242 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1066 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1049 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 2WKJ · 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 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 2WKJ · PDBe 2WKJ · UniProt P0A6L4
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