Research workbench
Capsid structure of a freshwater cyanophage siphoviridae MIC1
Analyse Capsid structure of a freshwater cyanophage siphoviridae MIC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J3Q
- Type
- protein
- Length
- 5,748 residues
- Chains
- 26
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein; Cement protein
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 17% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, U, V, W, X, Y, Z | Major capsid protein | protein | 346 | 15% helix, 17% strand | — |
| a | Major capsid protein | protein | 335 | 15% helix, 18% strand | — |
| 0, 3, 1, 4, 2, 6, 5, 7, b, 8, c, 9, d | Cement protein | protein | 97 | 29% helix, 9% strand | — |
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 | 239 | 0.83 | 0.96 | 62 | empty |
| 2 | 1104 | 0.81 | 0.82 | 88 | empty |
| 3 | 1196 | 0.80 | 0.81 | 117 | empty |
| 4 | 1000 | 0.79 | 0.81 | 88 | empty |
| 5 | 1063 | 0.79 | 0.81 | 98 | empty |
Interfaces
82 interfaces between chains.
- U–Z · 2960 Ų buried · 48 hydrogen bonds · protein-protein
- A–F · 2948 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 2936 Ų buried · 52 hydrogen bonds · protein-protein
- W–X · 2914 Ų buried · 45 hydrogen bonds · protein-protein
- U–V · 2901 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6J3Q · Capsid structure of a freshwater cyanophage Siphoviridae Mic1 · 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
- Elsewhere: RCSB PDB 6J3Q · PDBe 6J3Q
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