MolNFT v1 · #116974 · protein
First condensation domain of the calcium-dependent antibiotic synthetase in complex with substrate analogue 3A
5DUA · Cda peptide synthetase I: “First condensation domain of the calcium-dependent antibiotic synthetase in complex with substrate analogue 3A”. X-ray diffraction, 2 ligands (5FQ, CL), 10 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 5DUA
- Type
- protein
- Length
- 882 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cda peptide synthetase I
- UniProt
- Q9Z4X6
- Ligands
- 5FQ, CL
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cda peptide synthetase I | protein | 445 | 38% helix, 23% strand | Q9Z4X6 |
| B | Cda peptide synthetase I | protein | 437 | 39% helix, 24% strand | Q9Z4X6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.85 | 0.92 | 83 | 5FQ |
| 2 | 317 | 0.80 | 0.91 | 52 | CL, 5FQ |
| 3 | 61 | 0.56 | 0.89 | 20 | empty |
| 4 | 110 | 0.56 | 0.84 | 23 | empty |
| 5 | 65 | 0.55 | 0.88 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 805 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5DUA · 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 5DUA · PDBe 5DUA · UniProt Q9Z4X6
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