Research workbench
Crystal structure of the francisella novicida lysine decarboxylase ldcf
Analyse Crystal structure of the francisella novicida lysine decarboxylase ldcf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y3X
- Type
- protein
- Length
- 3,585 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine decarboxylase
- UniProt
- A0Q584
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Lysine decarboxylase | protein | 717 | 41% helix, 16% strand | A0Q584 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.75 | 0.78 | 103 | empty |
| 2 | 975 | 0.75 | 0.78 | 93 | empty |
| 3 | 635 | 0.75 | 0.81 | 79 | empty |
| 4 | 649 | 0.74 | 0.81 | 67 | empty |
| 5 | 224 | 0.66 | 0.84 | 41 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1214 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 1157 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 1142 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1139 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1102 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (cofactor).
Compared structures
- 6Y3X · Crystal structure of the Francisella novicida lysine decarboxylase LdcF · 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 A0Q584
- Elsewhere: RCSB PDB 6Y3X · PDBe 6Y3X · UniProt A0Q584
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