MolNFT v1 · #71519 · protein
D-peptide inhibitor PIE71 in complex with IQN17
3MGN: “D-peptide inhibitor PIE71 in complex with IQN17”. X-ray diffraction, 3 ligands (ACE, DLY, NH2), 1 pocket (best druggability 0.64). MolNFT v1 #71519 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3MGN
- Type
- protein
- Length
- 347 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IQN17; D-peptide inhibitor PIE71
- Ligands
- ACE, DLY, NH2
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | IQN17 | protein | 45 | 96% helix, 0% strand | — |
| G, L | D-peptide inhibitor PIE71 | protein | 13 | 54% helix, 0% strand | — |
| H, K | D-peptide inhibitor PIE71 | protein | 14 | 50% helix, 0% strand | — |
| I | D-peptide inhibitor PIE71 | protein | 12 | 58% helix, 0% strand | — |
| J | D-peptide inhibitor PIE71 | protein | 11 | 64% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 6 copies · chains A, B, C, D, E, F
- DLY · D-lysine · ligand · chains B, K
- NH2 · Amino group · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.64 | 0.75 | 54 | DLY |
Interfaces
22 interfaces between chains.
- E–F · 1007 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 1002 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 993 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 985 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 952 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 75 d-amino, 6 covalent, 6 disulfide (D-amino acid, covalent ligand, disulfide).
Compared structures
- 3MGN · D-Peptide inhibitor PIE71 in complex with IQN17 · the same entry in another collection · chain B against B, 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 3MGN · PDBe 3MGN
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