Research workbench
Wt hbc capsid like particles in complex with inhibitory peptide sllgrm and triton X-100
Analyse Wt hbc capsid like particles in complex with inhibitory peptide sllgrm and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PZN
- Type
- protein
- Length
- 576 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Sllgrm, modelled as poly-A,SLLGRM, modelled as poly-a
- UniProt
- P03146
- Ligands
- TRT
- Pockets
- 7 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 61% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | Capsid protein | protein | 143 | 63% helix, 0% strand | P03146 |
| M | Sllgrm, modelled as poly-A,SLLGRM, modelled as poly-a | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- TRT · Fragment of triton X-100 · ligand · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.78 | 0.95 | 28 | empty |
| 2 | 188 | 0.70 | 0.87 | 18 | TRT |
| 3 | 180 | 0.69 | 0.87 | 18 | TRT |
| 4 | 179 | 0.69 | 0.87 | 21 | TRT |
| 5 | 186 | 0.67 | 0.86 | 26 | TRT |
Interfaces
6 interfaces between chains.
- B–A · 2058 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1960 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 702 Ų buried · 5 hydrogen bonds · protein-protein
- D–M · 174 Ų buried · 2 hydrogen bonds · protein-protein
- C–M · 174 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7PZN · wt HBc capsid like particles in complex with inhibitory peptide SLLGRM and Triton X-100 · 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 P03146
- Elsewhere: RCSB PDB 7PZN · PDBe 7PZN · UniProt P03146
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