Research workbench
Crystal structure of class II lanthipeptide synthetase cylm in complex with AMP
Analyse Crystal structure of class II lanthipeptide synthetase cylm in complex with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DZT
- Type
- protein
- Length
- 886 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cylm
- UniProt
- Q8KUA3
- Ligands
- AMP, ZN
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cylm | protein | 886 | 53% helix, 7% strand | Q8KUA3 |
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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.72 | 0.78 | 74 | empty |
| 2 | 256 | 0.71 | 0.86 | 34 | empty |
| 3 | 425 | 0.67 | 0.79 | 51 | AMP |
| 4 | 166 | 0.58 | 0.82 | 21 | empty |
| 5 | 62 | 0.50 | 0.85 | 18 | empty |
Compared structures
- 5DZT · Crystal structure of class II lanthipeptide synthetase CylM in complex with AMP · 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 Q8KUA3
- Elsewhere: RCSB PDB 5DZT · PDBe 5DZT · UniProt Q8KUA3
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