Research workbench
Crystal structure of the V325G mutant of the bacteriophage G20C portal protein
Analyse Crystal structure of the V325G mutant of the bacteriophage G20C portal protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NGD
- Type
- protein
- Length
- 1,607 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Portal protein
- UniProt
- A7XXR3
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Portal protein | protein | 402 | 46% helix, 17% strand | A7XXR3 |
| B, C | Portal protein | protein | 401 | 46% helix, 18% strand | A7XXR3 |
| D | Portal protein | protein | 403 | 46% helix, 18% strand | A7XXR3 |
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.89 | 0.90 | 115 | empty |
| 2 | 1126 | 0.86 | 0.87 | 127 | empty |
| 3 | 363 | 0.85 | 0.94 | 57 | empty |
| 4 | 631 | 0.84 | 0.88 | 85 | empty |
| 5 | 227 | 0.76 | 0.91 | 42 | empty |
Interfaces
5 interfaces between chains.
- C–D · 5402 Ų buried · 63 hydrogen bonds · protein-protein
- B–C · 5334 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 5242 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 47 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5NGD · Crystal structure of the V325G mutant of the bacteriophage G20C portal protein · 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 A7XXR3
- Elsewhere: RCSB PDB 5NGD · PDBe 5NGD · UniProt A7XXR3
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