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The 2.6A structure of infectious bursal virus derived T=1 particles
Analyse The 2.6A structure of infectious bursal virus derived T=1 particles in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GSY
- Type
- protein
- Length
- 8,583 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein
- UniProt
- P61825
- Ligands
- CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, H, I, J, K, L, M, N, O, S, T | Polyprotein | protein | 428 | 12% helix, 44% strand | P61825 |
| E, F, G, R | Polyprotein | protein | 433 | 12% helix, 45% strand | P61825 |
| P | Polyprotein | protein | 430 | 12% helix, 46% strand | P61825 |
| Q | Polyprotein | protein | 429 | 12% helix, 45% strand | P61825 |
Ligands and binding sites
- CA · Calcium ion · metal · 11 copies · chains A, E, B, C, J, D, F, I, K, G, H, N, L, M, R, O, P, Q, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.87 | 0.95 | 43 | empty |
| 2 | 398 | 0.86 | 0.95 | 43 | empty |
| 3 | 390 | 0.86 | 0.95 | 42 | empty |
| 4 | 1104 | 0.86 | 0.87 | 146 | empty |
| 5 | 1077 | 0.86 | 0.87 | 150 | empty |
Interfaces
50 interfaces between chains.
- M–R · 2607 Ų buried · 48 hydrogen bonds · protein-protein
- F–I · 2595 Ų buried · 47 hydrogen bonds · protein-protein
- P–Q · 2589 Ų buried · 44 hydrogen bonds · protein-protein
- G–N · 2587 Ų buried · 46 hydrogen bonds · protein-protein
- O–Q · 2581 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 2GSY · The 2.6A structure of Infectious Bursal Virus Derived T=1 Particles · 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 P61825
- Elsewhere: RCSB PDB 2GSY · PDBe 2GSY · UniProt P61825
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