MolNFT v1 · #72760 · protein
54-membered ring macrocyclic beta-sheet peptide
3NI3: “54-membered ring macrocyclic beta-sheet peptide”. X-ray diffraction, 1 ligand (HAO), 2 pockets (best druggability 0.85). MolNFT v1 #72760 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NI3
- Type
- protein
- Length
- 120 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 54-membered ring macrocyclic beta-sheet peptide
- Ligands
- HAO
- Pockets
- 2 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | 54-membered ring macrocyclic beta-sheet peptide | protein | 10 | 0% helix, 50% strand | — |
Ligands and binding sites
- HAO · {[3-(hydrazinocarbonyl)-4-methoxyphenyl]amino}(oxo) acetic acid · ligand · 24 copies · chains A, I, F, B, C, D, E, G, L, H, J, K
- IPA · Isopropyl alcohol · additive · 6 copies · chains A, I, J, B, F, G, H, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.85 | 0.93 | 39 | empty |
| 2 | 495 | 0.83 | 0.89 | 52 | HAO, IPA |
Interfaces
26 interfaces between chains.
- G–H · 353 Ų buried · 15 hydrogen bonds · protein-protein
- K–L · 332 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 331 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 326 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 326 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 covalent, 36 modified (covalent ligand, nonstandard).
Compared structures
- 3NI3 · 54-Membered ring macrocyclic beta-sheet peptide · the same entry in another collection · chain G against G, 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 3NI3 · PDBe 3NI3
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