Research workbench
Structure of the Y137A mutant of E. COLI N-acetylneuraminic acid lyase in complex with pyruvate, N-acetyl-D-mannosamine and N-acetylneuraminic acid
Analyse Structure of the Y137A mutant of E. COLI N-acetylneuraminic acid lyase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BWL
- Type
- protein
- Length
- 1,188 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
- SI3, MN9
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 299 | 52% 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 | 296 | 53% helix, 13% strand | P0A6L4 |
| D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 298 | 53% helix, 14% strand | P0A6L4 |
Ligands and binding sites
- SI3 · 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid · ligand · 3 copies · chains A, B, D
- MN9 · 2-(acetylamino)-2-deoxy-D-mannose · ligand · chains C
- 1PE · Pentaethylene glycol · additive · 2 copies · chains B, D, A, C
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 | 175 | 0.73 | 0.90 | 25 | empty |
| 2 | 187 | 0.71 | 0.88 | 27 | empty |
| 3 | 382 | 0.68 | 0.80 | 42 | SI3 |
| 4 | 297 | 0.65 | 0.81 | 31 | MN9 |
| 5 | 334 | 0.65 | 0.80 | 37 | 1PE, SI3 |
Interfaces
4 interfaces between chains.
- A–D · 1249 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1243 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1062 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1053 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 4BWL · Structure of the Y137A mutant of E. coli N-acetylneuraminic acid lyase in complex with… · the same entry in another collection · chain C against C, 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 4BWL · PDBe 4BWL · UniProt P0A6L4
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