MolNFT v1 · #6484 · protein
N-acetylneuraminate lyase in complex with pyruvate via borohydride reduction
1FDZ: “N-acetylneuraminate lyase in complex with pyruvate via borohydride reduction”. X-ray diffraction, 1 ligand (PYR), 14 pockets (best druggability 0.73). MolNFT v1 #6484 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1FDZ
- Type
- protein
- Length
- 1,166 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
- 14 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 292 | 54% helix, 13% strand | P0A6L4 |
| B, C | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 291 | 53% helix, 14% strand | P0A6L4 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.73 | 0.90 | 26 | empty |
| 2 | 234 | 0.72 | 0.88 | 32 | empty |
| 3 | 333 | 0.69 | 0.82 | 32 | empty |
| 4 | 347 | 0.68 | 0.81 | 37 | PYR |
| 5 | 328 | 0.68 | 0.82 | 32 | PYR |
Interfaces
4 interfaces between chains.
- A–D · 1228 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1186 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1036 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1035 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1FDZ · N-acetylneuraminate lyase in complex with pyruvate via borohydride reduction · 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 1FDZ · PDBe 1FDZ · UniProt P0A6L4
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