Research workbench
An octameric barrel state of a de novo coiled-coil assembly: cc-TYPE2- (LAID)4-L21K.
Analyse An octameric barrel state of a de novo coiled-coil assembly: cc-TYPE2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NFM
- Type
- protein
- Length
- 480 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cc-TYPE2-(LAID)4-L21K
- Ligands
- ACE
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 93% helix, 0% 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 | Cc-TYPE2-(LAID)4-L21K | protein | 30 | 93% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 16 copies · chains A, H, B, C, D, E, F, G, I, P, J, K, L, M, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.88 | 0.88 | 59 | empty |
| 2 | 1200 | 0.88 | 0.87 | 62 | empty |
| 3 | 195 | 0.52 | 0.77 | 31 | empty |
| 4 | 180 | 0.49 | 0.76 | 29 | empty |
| 5 | 70 | 0.30 | 0.74 | 10 | empty |
Interfaces
26 interfaces between chains.
- A–B · 884 Ų buried · 6 hydrogen bonds · protein-protein
- O–P · 861 Ų buried · 5 hydrogen bonds · protein-protein
- M–N · 858 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 857 Ų buried · 6 hydrogen bonds · protein-protein
- K–L · 846 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent (covalent ligand).
Compared structures
- 7NFM · An octameric barrel state of a de novo coiled-coil assembly: CC-Type2-(LaId)4-L21K. · 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 7NFM · PDBe 7NFM
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