MolNFT v1 · #116973 · protein
First condensation domain of the calcium-dependent antibiotic synthetase in complex with substrate analogue 2A
5DU9 · Cda peptide synthetase I: “First condensation domain of the calcium-dependent antibiotic synthetase in complex with substrate analogue 2A”. X-ray diffraction, 3 ligands (UM2, CL, SO4), 10 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 5DU9
- Type
- protein
- Length
- 856 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cda peptide synthetase I
- UniProt
- Q9Z4X6
- Ligands
- UM2, CL, SO4
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cda peptide synthetase I | protein | 427 | 40% helix, 24% strand | Q9Z4X6 |
| B | Cda peptide synthetase I | protein | 429 | 40% helix, 23% strand | Q9Z4X6 |
Ligands and binding sites
- UM2 · (2S)-2-amino-N-butyl-propanamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.86 | 0.89 | 127 | CL, UM2 |
| 2 | 479 | 0.83 | 0.90 | 72 | CL, UM2 |
| 3 | 94 | 0.54 | 0.84 | 21 | empty |
| 4 | 92 | 0.52 | 0.83 | 21 | empty |
| 5 | 61 | 0.51 | 0.86 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 753 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5DU9 · First condensation domain of the calcium-dependent antibiotic synthetase in complex with… · 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 Q9Z4X6
- Elsewhere: RCSB PDB 5DU9 · PDBe 5DU9 · UniProt Q9Z4X6
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