Research workbench
Acidic stable capsid structure of helicobacter pylori bacteriophage KHP30
Analyse Acidic stable capsid structure of helicobacter pylori bacteriophage KHP30 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DN2
- Type
- protein
- Length
- 4,441 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major structural protein ORF14; Cement protein GP15
- UniProt
- I7H0H9, I7HFW5
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 9 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Major structural protein ORF14 | protein | 368 | 23% helix, 31% strand | I7H0H9 |
| b | Major structural protein ORF14 | protein | 366 | 26% helix, 28% strand | I7H0H9 |
| c | Major structural protein ORF14 | protein | 368 | 24% helix, 32% strand | I7H0H9 |
| d | Major structural protein ORF14 | protein | 371 | 23% helix, 31% strand | I7H0H9 |
| e, f | Major structural protein ORF14 | protein | 370 | 24% helix, 29% strand | I7H0H9 |
| g | Major structural protein ORF14 | protein | 370 | 25% helix, 28% strand | I7H0H9 |
| h | Major structural protein ORF14 | protein | 362 | 24% helix, 31% strand | I7H0H9 |
| i | Major structural protein ORF14 | protein | 362 | 21% helix, 25% strand | I7H0H9 |
| 1, 2, 3, 4, 5, 6, 7, 8, 9 | Cement protein GP15 | protein | 126 | 3% helix, 54% strand | I7HFW5 |
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 | 131 | 0.79 | 0.97 | 35 | empty |
| 2 | 867 | 0.79 | 0.82 | 95 | empty |
| 3 | 523 | 0.79 | 0.85 | 62 | empty |
| 4 | 124 | 0.78 | 0.97 | 24 | empty |
| 5 | 104 | 0.78 | 0.98 | 29 | empty |
Interfaces
51 interfaces between chains.
- b–c · 3620 Ų buried · 34 hydrogen bonds · protein-protein
- g–h · 3574 Ų buried · 26 hydrogen bonds · protein-protein
- e–f · 3521 Ų buried · 32 hydrogen bonds · protein-protein
- a–b · 3505 Ų buried · 32 hydrogen bonds · protein-protein
- d–e · 3475 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 7DN2 · Acidic stable capsid structure of Helicobacter pylori bacteriophage KHP30 · the same entry in another collection · chain 3 against 3, 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 I7H0H9
- Every structure of UniProt I7HFW5
- Elsewhere: RCSB PDB 7DN2 · PDBe 7DN2 · UniProt I7H0H9 · UniProt I7HFW5
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