Research workbench
A case study for twinned data analysis: multiple crystal forms of the enzyme N-acetyl-neuraminic lyase
Analyse A case study for twinned data analysis: multiple crystal forms of the enzyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UUI
- Type
- protein
- Length
- 1,196 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, NA
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 300 | 55% helix, 13% strand | P0A6L4 |
| B | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 298 | 55% helix, 13% strand | P0A6L4 |
| C, D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 299 | 54% helix, 13% strand | P0A6L4 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.76 | 0.91 | 27 | empty |
| 2 | 179 | 0.74 | 0.91 | 25 | empty |
| 3 | 321 | 0.68 | 0.82 | 30 | PYR |
| 4 | 424 | 0.67 | 0.79 | 40 | PYR |
| 5 | 378 | 0.67 | 0.80 | 36 | PYR |
Interfaces
4 interfaces between chains.
- A–D · 1262 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1246 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1050 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1045 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 4UUI · A case study for twinned data analysis: multiple crystal forms of the enzyme… · the same entry in another collection · chain A 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 4UUI · PDBe 4UUI · UniProt P0A6L4
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