Research workbench
Peptidyl-cysteine decarboxylase epid
Analyse Peptidyl-cysteine decarboxylase epid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1G63
- Type
- protein
- Length
- 1,983 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermin modifying enzyme epid
- UniProt
- P30197
- Ligands
- FMN
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, H, I, J, L | Epidermin modifying enzyme epid | protein | 164 | 45% helix, 18% strand | P30197 |
| B, F | Epidermin modifying enzyme epid | protein | 174 | 41% helix, 22% strand | P30197 |
| C, E, K | Epidermin modifying enzyme epid | protein | 163 | 45% helix, 18% strand | P30197 |
| D | Epidermin modifying enzyme epid | protein | 162 | 45% helix, 17% strand | P30197 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 12 copies · chains A, B, G, H, K, C, J, D, E, F, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.84 | 0.85 | 102 | FMN |
| 2 | 77 | 0.75 | 0.98 | 22 | empty |
| 3 | 65 | 0.75 | 0.99 | 20 | empty |
| 4 | 686 | 0.74 | 0.80 | 57 | FMN |
| 5 | 435 | 0.73 | 0.83 | 41 | FMN |
Interfaces
30 interfaces between chains.
- F–G · 912 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 879 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 857 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 856 Ų buried · 8 hydrogen bonds · protein-protein
- C–J · 853 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1G63 · Peptidyl-cysteine decarboxylase epid · the same entry in another collection · chain L against L, 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 P30197
- Elsewhere: RCSB PDB 1G63 · PDBe 1G63 · UniProt P30197
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