Research workbench
Structural analysis of PRD1
Analyse Structural analysis of PRD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W8X
- Type
- protein
- Length
- 4,903 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein (protein P3); Protein P30; Protein P31; Protein P16
- UniProt
- P22535, P27391, P27384, P27392
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 12 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein (protein P3) | protein | 380 | 15% helix, 42% strand | P22535 |
| B, D, H, I | Major capsid protein (protein P3) | protein | 392 | 16% helix, 41% strand | P22535 |
| C | Major capsid protein (protein P3) | protein | 385 | 17% helix, 41% strand | P22535 |
| E | Major capsid protein (protein P3) | protein | 378 | 17% helix, 42% strand | P22535 |
| F | Major capsid protein (protein P3) | protein | 388 | 16% helix, 40% strand | P22535 |
| G | Major capsid protein (protein P3) | protein | 375 | 14% helix, 42% strand | P22535 |
| J | Major capsid protein (protein P3) | protein | 390 | 15% helix, 40% strand | P22535 |
| K | Major capsid protein (protein P3) | protein | 384 | 17% helix, 40% strand | P22535 |
| L | Major capsid protein (protein P3) | protein | 379 | 17% helix, 39% strand | P22535 |
| M | Protein P30 | protein | 83 | 0% helix, 1% strand | P27391 |
| N | Protein P31 | protein | 114 | 0% helix, 29% strand | P27384 |
| P | Protein P16 | protein | 79 | 42% helix, 0% strand | P27392 |
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 | 935 | 0.89 | 0.91 | 132 | empty |
| 2 | 1026 | 0.85 | 0.86 | 119 | empty |
| 3 | 347 | 0.81 | 0.91 | 61 | empty |
| 4 | 498 | 0.81 | 0.88 | 58 | empty |
| 5 | 485 | 0.78 | 0.85 | 41 | empty |
Interfaces
32 interfaces between chains.
- J–K · 2007 Ų buried · 42 hydrogen bonds · protein-protein
- G–I · 2002 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 1980 Ų buried · 42 hydrogen bonds · protein-protein
- H–I · 1963 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 1957 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 1W8X · Structural analysis of PRD1 · the same entry in another collection · chain D against D, 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
- Every structure of UniProt P27391
- Every structure of UniProt P27384
- Every structure of UniProt P27392
- Elsewhere: RCSB PDB 1W8X · PDBe 1W8X · UniProt P22535 · UniProt P27391 · UniProt P27384 · UniProt P27392
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