Research workbench
Topological model of the P2 virion baseplate in activated conformation (closed tal trimer)
Analyse Topological model of the P2 virion baseplate in activated conformation (closed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZIG
- Type
- protein
- Length
- 9,435 residues
- Chains
- 33
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor binding protein; Distal tail protein; Baseplate protein GP16
- UniProt
- Q71AW2, D3WAD3, D3KFX4
- Pockets
- 20 · best druggability 0.55
Structure
electron microscopy · 3 distinct chains · 0% helix, 0% 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 | Receptor binding protein | protein | 263 | 0% helix, 0% strand | Q71AW2 |
| S, T, U, V, W, X, 2, 3, 4, 5, 6, 7 | Distal tail protein | protein | 298 | 0% helix, 0% strand | D3WAD3 |
| Y, Z, 1 | Baseplate protein GP16 | protein | 375 | 0% helix, 0% strand | D3KFX4 |
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 | 321 | 0.55 | 0.73 | 70 | empty |
| 2 | 255 | 0.53 | 0.74 | 53 | empty |
| 3 | 234 | 0.52 | 0.74 | 50 | empty |
| 4 | 236 | 0.51 | 0.73 | 52 | empty |
| 5 | 202 | 0.49 | 0.74 | 50 | empty |
Interfaces
65 interfaces between chains.
- B–C · 575 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 575 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 573 Ų buried · 0 hydrogen bonds · protein-protein
- K–L · 571 Ų buried · 0 hydrogen bonds · protein-protein
- N–O · 570 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ZIG · Topological model of the p2 virion baseplate in activated conformation (closed Tal trimer) · the same entry in another collection · chain B against B, 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 Q71AW2
- Every structure of UniProt D3WAD3
- Every structure of UniProt D3KFX4
- Elsewhere: RCSB PDB 6ZIG · PDBe 6ZIG · UniProt Q71AW2 · UniProt D3WAD3 · UniProt D3KFX4
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