MolNFT v1 · #108999 · protein
Crystal structures of cdnal from clostridium difficile in complex with ketobutyric
4WOQ · N-acetylneuraminate lyase: “Crystal structures of cdnal from clostridium difficile in complex with ketobutyric”. X-ray diffraction, 1 ligand (2KT), 20 pockets (best druggability 0.88). MolNFT v1 #108999 on GenesisL1: 3D structure…
- PDB
- 4WOQ
- Type
- protein
- Length
- 2,320 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
- 2KT
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 290 | 51% helix, 14% strand | D5Q364 |
Ligands and binding sites
- 2KT · 2-ketobutyric acid · ligand · 8 copies · chains A, D, B, C, E, F, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.88 | 0.89 | 109 | empty |
| 2 | 174 | 0.71 | 0.89 | 28 | empty |
| 3 | 200 | 0.70 | 0.87 | 31 | empty |
| 4 | 380 | 0.69 | 0.81 | 41 | empty |
| 5 | 392 | 0.68 | 0.81 | 36 | empty |
Interfaces
11 interfaces between chains.
- C–G · 1587 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 1578 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 1569 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 1553 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 1156 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4WOQ · Crystal Structures of CdNal from Clostridium difficile in complex with ketobutyric · 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 4WOQ · PDBe 4WOQ · UniProt D5Q364
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