Research workbench
Quasi-atomic resolution model of bacteriophage PRD1 capsid, obtained by combined cryo-EM and X-ray crystallography.
Analyse Quasi-atomic resolution model of bacteriophage PRD1 capsid, obtained by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GW7
- Type
- protein
- Length
- 4,451 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- P22535
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, J | Major capsid protein | protein | 370 | 14% helix, 42% strand | P22535 |
| B, E, H, K | Major capsid protein | protein | 372 | 15% helix, 42% strand | P22535 |
| C, F, I, L | Major capsid protein | protein | 371 | 16% helix, 43% strand | P22535 |
| D | Major capsid protein | protein | 369 | 14% helix, 42% strand | P22535 |
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 | 1059 | 0.85 | 0.86 | 86 | empty |
| 2 | 862 | 0.80 | 0.83 | 86 | empty |
| 3 | 1089 | 0.79 | 0.81 | 96 | empty |
| 4 | 888 | 0.78 | 0.80 | 85 | empty |
| 5 | 202 | 0.77 | 0.92 | 28 | empty |
Interfaces
22 interfaces between chains.
- A–C · 1777 Ų buried · 33 hydrogen bonds · protein-protein
- G–I · 1777 Ų buried · 33 hydrogen bonds · protein-protein
- D–F · 1775 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1770 Ų buried · 36 hydrogen bonds · protein-protein
- J–L · 1768 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 1GW7 · Quasi-atomic resolution model of bacteriophage PRD1 capsid, obtained by combined cryo-EM… · 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 P22535
- Elsewhere: RCSB PDB 1GW7 · PDBe 1GW7 · UniProt P22535
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.