MolNFT v1 · #117157 · protein
Crystal structure of class II lanthipeptide synthetase cylm in complex with AMP
5DZT: “Crystal structure of class II lanthipeptide synthetase cylm in complex with AMP”. X-ray diffraction, 2 ligands (AMP, ZN), 10 pockets (best druggability 0.72). MolNFT v1 #117157 on GenesisL1: 3D structure, binding sites and pockets…
- 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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