MolNFT v1 · #166118 · protein
C3 symmetric peptide design number 3
6UGC · C3-3 cyclic peptide design: “C3 symmetric peptide design number 3”. X-ray diffraction, 2 ligands (NA, CD), 1 pocket (best druggability 0.39). MolNFT v1 #166118 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6UGC
- Type
- protein
- Length
- 81 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C3-3 cyclic peptide design
- Ligands
- NA, CD
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | C3-3 cyclic peptide design | protein | 9 | 0% helix, 0% strand | — |
| I, J, K | C3-3 cyclic peptide design | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 22 copies · chains A, K, B, C, D, E, I, F, G, H, J
- CD · Cadmium ion · metal · 6 copies · chains A, C, D, B, E, G, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.39 | 0.75 | 23 | NA |
Interfaces
19 interfaces between chains.
- B–C · 199 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 198 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 195 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 194 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6UGC · C3 symmetric peptide design number 3 · 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 6UGC · PDBe 6UGC
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