Research workbench
Crystal structure of bacteriophage HK97 GP6
Analyse Crystal structure of bacteriophage HK97 GP6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JVO
- Type
- protein
- Length
- 1,247 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP6
- UniProt
- Q9MBY2
- Ligands
- CL
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, H, J, K, L, M | GP6 | protein | 96 | 58% helix, 4% strand | Q9MBY2 |
| C | GP6 | protein | 95 | 59% helix, 4% strand | Q9MBY2 |
| G | GP6 | protein | 97 | 58% helix, 4% strand | Q9MBY2 |
| I | GP6 | protein | 95 | 59% helix, 4% strand | Q9MBY2 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains I, L
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, B, M, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.71 | 0.96 | 15 | MPD |
| 2 | 85 | 0.68 | 0.93 | 16 | MPD |
| 3 | 59 | 0.68 | 0.95 | 14 | empty |
| 4 | 91 | 0.67 | 0.92 | 17 | empty |
| 5 | 109 | 0.66 | 0.90 | 21 | empty |
Interfaces
26 interfaces between chains.
- H–I · 1383 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1371 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1358 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1355 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1352 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 modified (engineered).
Compared structures
- 3JVO · Crystal structure of bacteriophage HK97 gp6 · 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 Q9MBY2
- Elsewhere: RCSB PDB 3JVO · PDBe 3JVO · UniProt Q9MBY2
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