Research workbench
Crystal structures of cdnal from clostridium difficile in complex with mannosamine
Analyse Crystal structures of cdnal from clostridium difficile in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WOZ
- Type
- protein
- Length
- 2,319 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylneuraminate lyase
- EC
- 4.1.3.3
- UniProt
- D5Q364
- Ligands
- MN9
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 290 | 53% helix, 14% strand | D5Q364 |
| C | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 289 | 51% helix, 15% strand | D5Q364 |
Ligands and binding sites
- MN9 · 2-(acetylamino)-2-deoxy-D-mannose · ligand · 2 copies · chains A, B, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.75 | 0.92 | 26 | empty |
| 2 | 180 | 0.75 | 0.91 | 27 | empty |
| 3 | 176 | 0.71 | 0.89 | 30 | empty |
| 4 | 188 | 0.71 | 0.89 | 34 | empty |
| 5 | 415 | 0.71 | 0.81 | 38 | empty |
Interfaces
11 interfaces between chains.
- B–C · 1595 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1564 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1563 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 1545 Ų buried · 14 hydrogen bonds · protein-protein
- D–G · 1190 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4WOZ · Crystal Structures of CdNal from Clostridium difficile in complex with mannosamine · 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 D5Q364
- Elsewhere: RCSB PDB 4WOZ · PDBe 4WOZ · UniProt D5Q364
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