Research workbench
Exploring the atomic structure and conformational flexibility of a 320 ångström long engineered viral fiber using X-ray crystallography
Analyse Exploring the atomic structure and conformational flexibility of a 320 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LIN
- Type
- protein
- Length
- 3,468 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tail needle protein GP26
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Tail needle protein GP26 | protein | 289 | 65% helix, 5% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.76 | 0.79 | 100 | empty |
| 2 | 68 | 0.73 | 0.97 | 19 | empty |
| 3 | 471 | 0.61 | 0.75 | 49 | empty |
| 4 | 625 | 0.61 | 0.73 | 71 | empty |
| 5 | 373 | 0.54 | 0.74 | 49 | empty |
Interfaces
34 interfaces between chains.
- B–C · 6308 Ų buried · 71 hydrogen bonds · protein-protein
- A–C · 6304 Ų buried · 79 hydrogen bonds · protein-protein
- D–F · 6259 Ų buried · 78 hydrogen bonds · protein-protein
- J–L · 6237 Ų buried · 73 hydrogen bonds · protein-protein
- E–F · 6197 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 4LIN · Exploring the atomic structure and conformational flexibility of a 320 angstrom long… · 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 4LIN · PDBe 4LIN
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