Research workbench
Topological model of P2 virion baseplate in resting conformation
Analyse Topological model of P2 virion baseplate in resting conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZJJ
- Type
- protein
- Length
- 9,435 residues
- Chains
- 33
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Distal tail protein; Receptor binding protein; Baseplate protein GP16
- UniProt
- D3WAD3, Q71AW2, D3KFX4
- Pockets
- 20 · best druggability 0.61
Structure
electron microscopy · 3 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T, S, U, V, W, X, 2, 3, 4, 5, 6, 7 | Distal tail protein | protein | 298 | 0% helix, 0% strand | D3WAD3 |
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R | Receptor binding protein | protein | 263 | 0% helix, 0% strand | Q71AW2 |
| Y, Z, 1 | Baseplate protein GP16 | protein | 375 | 0% helix, 0% strand | D3KFX4 |
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 | 460 | 0.61 | 0.73 | 79 | empty |
| 2 | 395 | 0.59 | 0.73 | 84 | empty |
| 3 | 386 | 0.59 | 0.73 | 75 | empty |
| 4 | 335 | 0.57 | 0.74 | 68 | empty |
| 5 | 324 | 0.56 | 0.73 | 67 | empty |
Interfaces
57 interfaces between chains.
- M–N · 572 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 570 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 569 Ų buried · 0 hydrogen bonds · protein-protein
- P–Q · 569 Ų buried · 0 hydrogen bonds · protein-protein
- J–K · 569 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZJJ · Topological model of p2 virion baseplate in resting conformation · 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 D3WAD3
- Every structure of UniProt Q71AW2
- Every structure of UniProt D3KFX4
- Elsewhere: RCSB PDB 6ZJJ · PDBe 6ZJJ · UniProt D3WAD3 · UniProt Q71AW2 · UniProt D3KFX4
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