MolNFT v1 · #101514 · protein
Crystal structure of macrocycles containing a 17-23 (LV(PHI)FAED) and a 30-36 (AII(SAR)L(ORN)V)
4NTP · Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN) V: “Crystal structure of macrocycles containing a 17-23 (LV(PHI)FAED) and a 30-36 (AII(SAR)L(ORN)V)”. X-ray diffraction, 2 ligands (NA, CL), 1 pocket (best druggability…
- PDB
- 4NTP
- Type
- protein
- Length
- 256 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN) V
- Ligands
- NA, CL
- Pockets
- 1 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Cyclic hexadecapeptide (ORN)LV(PHI)FAED(ORN)AII(SAR)L(ORN) V | protein | 16 | 0% helix, 63% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C, D, F, E, L
- CL · Chloride ion · ion · 5 copies · chains B, E, G, H, P
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 | 1181 | 0.85 | 0.85 | 104 | NA |
Interfaces
37 interfaces between chains.
- E–F · 240 Ų buried · 2 hydrogen bonds · protein-protein
- J–K · 239 Ų buried · 2 hydrogen bonds · protein-protein
- H–I · 236 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 236 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 234 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 80 modified (nonstandard, methylation).
Compared structures
- 4NTP · Crystal structure of macrocycles containing A 17-23 (LV(PHI)FAED) and A 30-36… · the same entry in another collection · chain F against F, 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 4NTP · PDBe 4NTP
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