MolNFT v1 · #72394 · protein
X-ray crystal structure of the escherichia COLI inducible lysine decarboxylase ldci
3N75 · Lysine decarboxylase, inducible: “X-ray crystal structure of the escherichia COLI inducible lysine decarboxylase ldci”. X-ray diffraction, 1 ligand (G4P), 20 pockets (best druggability 0.76). MolNFT v1 #72394 on GenesisL1: 3D…
- PDB
- 3N75
- Type
- protein
- Length
- 3,555 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine decarboxylase, inducible
- EC
- 4.1.1.18
- UniProt
- P0A9H3
- Ligands
- G4P
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Lysine decarboxylase, inducible (EC 4.1.1.18) | protein | 711 | 43% helix, 17% strand | P0A9H3 |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 5 copies · chains A, D, B, E, C
- P6G · Hexaethylene glycol · additive · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.76 | 0.78 | 88 | G4P |
| 2 | 1013 | 0.76 | 0.78 | 98 | empty |
| 3 | 964 | 0.76 | 0.78 | 82 | empty |
| 4 | 906 | 0.75 | 0.78 | 90 | empty |
| 5 | 462 | 0.74 | 0.83 | 49 | empty |
Interfaces
5 interfaces between chains.
- C–E · 1309 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1301 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1301 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1298 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 1295 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (cofactor).
Compared structures
- 3N75 · X-ray Crystal Structure of the Escherichia coli Inducible Lysine Decarboxylase LdcI · 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 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 P0A9H3
- Elsewhere: RCSB PDB 3N75 · PDBe 3N75 · UniProt P0A9H3
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