Research workbench
Cryo-EM structure of PCV2 vlps
Analyse Cryo-EM structure of PCV2 vlps in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZBO
- Type
- protein
- Length
- 10,860 residues
- Chains
- 60
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- G0Y2B2
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 2% helix, 27% 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, 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, y | Capsid protein | protein | 181 | 2% helix, 27% strand | G0Y2B2 |
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 | 140 | 0.80 | 0.97 | 25 | empty |
| 2 | 629 | 0.80 | 0.85 | 55 | empty |
| 3 | 621 | 0.80 | 0.85 | 56 | empty |
| 4 | 141 | 0.80 | 0.97 | 27 | empty |
| 5 | 629 | 0.80 | 0.85 | 59 | empty |
Interfaces
150 interfaces between chains.
- A–C · 1168 Ų buried · 13 hydrogen bonds · protein-protein
- m–y · 1167 Ų buried · 13 hydrogen bonds · protein-protein
- w–x · 1167 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 1167 Ų buried · 12 hydrogen bonds · protein-protein
- a–s · 1165 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5ZBO · Cryo-EM structure of PCV2 VLPs · the same entry in another collection · chain h against h, 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 G0Y2B2
- Elsewhere: RCSB PDB 5ZBO · PDBe 5ZBO · UniProt G0Y2B2
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