Research workbench
The de novo evolutionary emergence of a symmetrical protein is shaped by folding constraints
Analyse The de novo evolutionary emergence of a symmetrical protein is shaped by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C2N
- Type
- protein
- Length
- 700 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta propeller
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, O | Beta propeller | protein | 46 | 9% helix, 43% strand | — |
| B, C, E, F, H, I, K, L, M, N | Beta propeller | protein | 47 | 9% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, C, B, D, G, H, E, I, O, F, J, K, L, N, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.78 | 0.86 | 35 | empty |
| 2 | 460 | 0.78 | 0.85 | 35 | empty |
| 3 | 452 | 0.77 | 0.85 | 36 | empty |
| 4 | 269 | 0.63 | 0.81 | 39 | NAG |
| 5 | 321 | 0.62 | 0.79 | 48 | NAG |
Interfaces
23 interfaces between chains.
- F–H · 665 Ų buried · 2 hydrogen bonds · protein-protein
- E–I · 652 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 648 Ų buried · 5 hydrogen bonds · protein-protein
- M–O · 641 Ų buried · 3 hydrogen bonds · protein-protein
- F–J · 641 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5C2N · The de novo evolutionary emergence of a symmetrical protein is shaped by folding… · 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 5C2N · PDBe 5C2N
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