Research workbench
Focused refinement of asymmetric unit of bacteriophage lambda procapsid at 3.88 ångström
Analyse Focused refinement of asymmetric unit of bacteriophage lambda procapsid at 3.88… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VIA
- Type
- protein
- Length
- 2,345 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- P03713
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 22% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Major capsid protein | protein | 335 | 22% helix, 24% strand | P03713 |
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 | 955 | 0.86 | 0.87 | 120 | empty |
| 2 | 992 | 0.82 | 0.83 | 88 | empty |
| 3 | 627 | 0.81 | 0.86 | 85 | empty |
| 4 | 952 | 0.80 | 0.82 | 88 | empty |
| 5 | 512 | 0.80 | 0.87 | 73 | empty |
Interfaces
12 interfaces between chains.
- D–E · 2281 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2212 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 2158 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2141 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2138 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7VIA · Focused refinement of asymmetric unit of bacteriophage lambda procapsid at 3.88 Angstrom · 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 P03713
- Elsewhere: RCSB PDB 7VIA · PDBe 7VIA · UniProt P03713
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