Research workbench
The triple jelly roll fold and turret assembly in an archaeal virus
Analyse The triple jelly roll fold and turret assembly in an archaeal virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IND
- Type
- protein
- Length
- 7,540 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C381 turret protein
- UniProt
- Q6Q0L3
- Ligands
- 2HP
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 58% 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, Q, R, S, T | C381 turret protein | protein | 377 | 2% helix, 58% strand | Q6Q0L3 |
Ligands and binding sites
- 2HP · Dihydrogenphosphate ion · ion · 60 copies · chains A, E, B, C, D, F, J, G, H, I, K, O, L, M, N, P, T, Q, R, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.80 | 0.81 | 102 | empty |
| 2 | 620 | 0.66 | 0.77 | 41 | empty |
| 3 | 620 | 0.66 | 0.77 | 42 | empty |
| 4 | 600 | 0.66 | 0.77 | 40 | empty |
| 5 | 567 | 0.66 | 0.77 | 37 | empty |
Interfaces
30 interfaces between chains.
- P–Q · 2538 Ų buried · 60 hydrogen bonds · protein-protein
- F–G · 2535 Ų buried · 55 hydrogen bonds · protein-protein
- M–N · 2530 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 2529 Ų buried · 57 hydrogen bonds · protein-protein
- S–T · 2528 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 4IND · The Triple Jelly Roll Fold and Turret Assembly in an Archaeal Virus · 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
- Every structure of UniProt Q6Q0L3
- Elsewhere: RCSB PDB 4IND · PDBe 4IND · UniProt Q6Q0L3
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