MolNFT v1 · #59870 · protein
Crystal structure of lipopeptide detergent (lpd-12)
3CAY: “Crystal structure of lipopeptide detergent (lpd-12)”. X-ray diffraction, 2 ligands (ACE, NH2), 3 pockets (best druggability 0.82). MolNFT v1 #59870 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3CAY
- Type
- protein
- Length
- 300 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lpd-12
- Ligands
- ACE, NH2
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 92% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Lpd-12 | protein | 25 | 92% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NH2 · Amino group · ion · 12 copies · chains A, B, C, I, D, J, E, F, G, H, K, L
- LMT · Dodecyl-beta-D-maltoside · additive · 22 copies · chains A, B, F, G, H, C, D, E, I, K, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.82 | 0.84 | 68 | LMT |
| 2 | 183 | 0.66 | 0.86 | 24 | empty |
| 3 | 231 | 0.46 | 0.72 | 29 | LMT |
Interfaces
34 interfaces between chains.
- G–H · 729 Ų buried · 1 hydrogen bond · protein-protein
- K–L · 686 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 681 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 662 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 658 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified, 12 covalent (nonstandard, covalent ligand).
Compared structures
- 3CAY · Crystal structure of Lipopeptide Detergent (LPD-12) · 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
- Elsewhere: RCSB PDB 3CAY · PDBe 3CAY
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