Research workbench
Quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography.
Analyse Quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HB9
- Type
- protein
- Length
- 4,460 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriophage PRD1
- UniProt
- P22535
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Bacteriophage PRD1 | protein | 370 | 14% helix, 43% strand | P22535 |
| B, E, H, K | Bacteriophage PRD1 | protein | 374 | 14% helix, 43% strand | P22535 |
| C, F, I, L | Bacteriophage PRD1 | protein | 371 | 16% helix, 43% 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 | 509 | 0.82 | 0.88 | 62 | empty |
| 2 | 569 | 0.81 | 0.87 | 73 | empty |
| 3 | 561 | 0.81 | 0.87 | 85 | empty |
| 4 | 538 | 0.81 | 0.87 | 61 | empty |
| 5 | 521 | 0.78 | 0.85 | 44 | empty |
Interfaces
22 interfaces between chains.
- H–I · 1868 Ų buried · 37 hydrogen bonds · protein-protein
- K–L · 1866 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1861 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 1855 Ų buried · 37 hydrogen bonds · protein-protein
- G–I · 1789 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 1HB9 · quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by… · the same entry in another collection · chain L against L, 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 1HB9 · PDBe 1HB9 · UniProt P22535
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