Research workbench
Topological model of P2 virion baseplate in activated conformation
Analyse Topological model of P2 virion baseplate in activated conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZIH
- Type
- protein
- Length
- 9,426 residues
- Chains
- 33
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Distal tail protein; Baseplate protein GP16; Receptor binding protein
- UniProt
- D3WAD3, D3KFX4, Q71AW2
- Pockets
- 20 · best druggability 0.58
Structure
electron microscopy · 3 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2, 3, 7, 6, 5, 4, S, T, U, V, W, X | Distal tail protein | protein | 298 | 0% helix, 0% strand | D3WAD3 |
| 1, Y, Z | Baseplate protein GP16 | protein | 372 | 0% helix, 0% strand | D3KFX4 |
| 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 |
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.58 | 0.74 | 71 | empty |
| 2 | 326 | 0.56 | 0.73 | 61 | empty |
| 3 | 228 | 0.53 | 0.75 | 50 | empty |
| 4 | 238 | 0.52 | 0.74 | 45 | empty |
| 5 | 213 | 0.49 | 0.73 | 53 | empty |
Interfaces
74 interfaces between chains.
- E–F · 573 Ų buried · 0 hydrogen bonds · protein-protein
- J–K · 573 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 572 Ų buried · 0 hydrogen bonds · protein-protein
- N–O · 571 Ų buried · 0 hydrogen bonds · protein-protein
- K–L · 571 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZIH · Topological model of p2 virion baseplate in activated conformation · the same entry in another collection · chain 3 against 3, 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 D3KFX4
- Every structure of UniProt Q71AW2
- Elsewhere: RCSB PDB 6ZIH · PDBe 6ZIH · UniProt D3WAD3 · UniProt D3KFX4 · UniProt Q71AW2
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