Research workbench
High resolution cryo EM analysis of HPV16 identifies minor structural protein L2 and describes capsid flexibility
Analyse High resolution cryo EM analysis of HPV16 identifies minor structural protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KZF
- Type
- protein
- Length
- 2,864 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein L1
- UniProt
- P03101
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 11% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Major capsid protein L1 | protein | 483 | 11% helix, 35% strand | P03101 |
| B | Major capsid protein L1 | protein | 466 | 11% helix, 35% strand | P03101 |
| C, D | Major capsid protein L1 | protein | 480 | 10% helix, 33% strand | P03101 |
| E | Major capsid protein L1 | protein | 481 | 12% helix, 33% strand | P03101 |
| A | Major capsid protein L1 | protein | 474 | 11% helix, 30% strand | P03101 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.80 | 0.82 | 143 | empty |
| 2 | 986 | 0.70 | 0.75 | 52 | empty |
| 3 | 469 | 0.68 | 0.79 | 73 | empty |
| 4 | 475 | 0.68 | 0.79 | 62 | empty |
| 5 | 458 | 0.68 | 0.79 | 69 | empty |
Interfaces
12 interfaces between chains.
- B–C · 4156 Ų buried · 55 hydrogen bonds · protein-protein
- F–E · 4153 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 3988 Ų buried · 58 hydrogen bonds · protein-protein
- F–B · 3971 Ų buried · 56 hydrogen bonds · protein-protein
- D–E · 3915 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 7KZF · High resolution cryo EM analysis of HPV16 identifies minor structural protein L2 and… · the same entry in another collection · chain F against F, 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 P03101
- Elsewhere: RCSB PDB 7KZF · PDBe 7KZF · UniProt P03101
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