Research workbench
Revisited cryo-EM structure of inducible lysine decarboxylase complexed with lara domain of rava ATPase
Analyse Revisited cryo-EM structure of inducible lysine decarboxylase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FL2
- Type
- protein
- Length
- 816 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine decarboxylase, inducible; ATPase rava
- EC
- 4.1.1.18, 3.6.3.-
- UniProt
- P0A9H3, P31473
- Pockets
- 12 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine decarboxylase, inducible (EC 4.1.1.18) | protein | 710 | 42% helix, 16% strand | P0A9H3 |
| K | ATPase rava (EC 3.6.3.-) | protein | 106 | 9% helix, 42% strand | P31473 |
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.79 | 0.84 | 92 | empty |
| 2 | 605 | 0.74 | 0.81 | 77 | empty |
| 3 | 694 | 0.73 | 0.79 | 63 | empty |
| 4 | 428 | 0.72 | 0.82 | 58 | empty |
| 5 | 572 | 0.67 | 0.77 | 58 | empty |
Interfaces
1 interface between chains.
- A–K · 131 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FL2 · Revisited cryo-EM structure of Inducible lysine decarboxylase complexed with LARA domain… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A9H3 · AlphaFold monomer V2.0 prediction for inducible lysine decarboxylase (P0A9H3) · a predicted model of the same protein · chain A against A, TM-score 0.94
- P31473 · AlphaFold monomer V2.0 prediction for ATPase rava (P31473) · a predicted model of the same protein · chain K against A, TM-score 0.92
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 P0A9H3
- Every structure of UniProt P31473
- Elsewhere: RCSB PDB 5FL2 · PDBe 5FL2 · UniProt P0A9H3 · UniProt P31473
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