MolNFT v1 · #128095 · protein
Crystal structure of the V325G mutant of the bacteriophage G20C portal protein
5NGD: “Crystal structure of the V325G mutant of the bacteriophage G20C portal protein”. X-ray diffraction, 20 pockets (best druggability 0.89). MolNFT v1 #128095 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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