Research workbench
Structure of N-citrylornithine decarboxylase bound with plp
Analyse Structure of N-citrylornithine decarboxylase bound with plp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KH2
- Type
- protein
- Length
- 1,642 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-citrylornithine decarboxylase
- UniProt
- Q15EG8
- Ligands
- PLP, SO4
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-citrylornithine decarboxylase | protein | 409 | 33% helix, 25% strand | Q15EG8 |
| B | N-citrylornithine decarboxylase | protein | 409 | 35% helix, 26% strand | Q15EG8 |
| C | N-citrylornithine decarboxylase | protein | 409 | 34% helix, 25% strand | Q15EG8 |
| D | N-citrylornithine decarboxylase | protein | 415 | 34% helix, 25% strand | Q15EG8 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.81 | 0.83 | 102 | PLP, SO4 |
| 2 | 819 | 0.79 | 0.82 | 91 | PLP |
| 3 | 647 | 0.76 | 0.82 | 84 | empty |
| 4 | 306 | 0.66 | 0.81 | 47 | empty |
| 5 | 363 | 0.64 | 0.79 | 61 | empty |
Interfaces
5 interfaces between chains.
- B–D · 2351 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 2253 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 345 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 276 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 4 cofactor (engineered, pyridoxal phosphate Schiff base).
Compared structures
- 7KH2 · Structure of N-citrylornithine decarboxylase bound with PLP · 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 Q15EG8
- Elsewhere: RCSB PDB 7KH2 · PDBe 7KH2 · UniProt Q15EG8
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