Research workbench
Crystal structure of HPV16 L1 pentamer bound to heparin oligosaccharides
Analyse Crystal structure of HPV16 L1 pentamer bound to heparin oligosaccharides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W1O
- Type
- protein
- Length
- 2,131 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein L1
- UniProt
- Q81007
- Ligands
- JHM, IDS
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Major capsid protein L1 | protein | 427 | 12% helix, 37% strand | Q81007 |
| D | Major capsid protein L1 | protein | 425 | 13% helix, 37% strand | Q81007 |
| E | Major capsid protein L1 | protein | 425 | 15% helix, 37% strand | Q81007 |
Ligands and binding sites
- JHM · 2-deoxy-6-O-sulfo-alpha-D-glucopyranose · ligand · 13 copies · chains A, B, E, C, D
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 13 copies · chains A, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.69 | 0.74 | 65 | empty |
| 2 | 275 | 0.60 | 0.79 | 50 | empty |
| 3 | 267 | 0.60 | 0.79 | 49 | empty |
| 4 | 291 | 0.60 | 0.79 | 47 | empty |
| 5 | 233 | 0.56 | 0.78 | 37 | empty |
Interfaces
10 interfaces between chains.
- A–E · 3518 Ų buried · 66 hydrogen bonds · protein-protein
- B–C · 3510 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 3501 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 3489 Ų buried · 64 hydrogen bonds · protein-protein
- D–E · 3487 Ų buried · 65 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 2 covalent (covalent ligand, glycosylation, N-glycosylation).
Compared structures
- 5W1O · Crystal Structure of HPV16 L1 Pentamer Bound to Heparin Oligosaccharides · 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 Q81007
- Elsewhere: RCSB PDB 5W1O · PDBe 5W1O · UniProt Q81007
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