Research workbench
T=1 subviral particle of grouper nervous necrosis virus capsid protein deletion mutant (delta 1-34 & 218-338)
Analyse T=1 subviral particle of grouper nervous necrosis virus capsid protein deletion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RFT
- Type
- protein
- Length
- 9,780 residues
- Chains
- 60
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein
- UniProt
- Q8JNX5
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 39% 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, U, V, W, X, Y, Z, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x | Coat protein | protein | 163 | 9% helix, 39% strand | Q8JNX5 |
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 | 435 | 0.71 | 0.82 | 64 | empty |
| 2 | 55 | 0.69 | 0.97 | 13 | empty |
| 3 | 473 | 0.69 | 0.80 | 57 | empty |
| 4 | 353 | 0.68 | 0.82 | 45 | empty |
| 5 | 383 | 0.68 | 0.81 | 53 | empty |
Interfaces
203 interfaces between chains.
- c–s · 769 Ų buried · 11 hydrogen bonds · protein-protein
- 4–9 · 764 Ų buried · 12 hydrogen bonds · protein-protein
- d–x · 763 Ų buried · 12 hydrogen bonds · protein-protein
- H–N · 763 Ų buried · 12 hydrogen bonds · protein-protein
- S–T · 761 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4RFT · T=1 subviral particle of Grouper nervous necrosis virus capsid protein deletion mutant… · the same entry in another collection · chain O against O, 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 Q8JNX5
- Elsewhere: RCSB PDB 4RFT · PDBe 4RFT · UniProt Q8JNX5
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