MolNFT v1 · #152400 · protein
Crystal structure of HPV58/33 chimeric L1 pentamer
6IGD · Major capsid protein L1: “Crystal structure of HPV58/33 chimeric L1 pentamer”. X-ray diffraction, 20 pockets (best druggability 0.68). MolNFT v1 #152400 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IGD
- Type
- protein
- Length
- 4,162 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein L1
- UniProt
- P26535
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 7 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, I | Major capsid protein L1 | protein | 416 | 14% helix, 39% strand | P26535 |
| B, G | Major capsid protein L1 | protein | 414 | 16% helix, 41% strand | P26535 |
| C | Major capsid protein L1 | protein | 415 | 15% helix, 39% strand | P26535 |
| D | Major capsid protein L1 | protein | 416 | 15% helix, 39% strand | P26535 |
| E | Major capsid protein L1 | protein | 420 | 14% helix, 39% strand | P26535 |
| H | Major capsid protein L1 | protein | 414 | 15% helix, 40% strand | P26535 |
| J | Major capsid protein L1 | protein | 421 | 15% helix, 39% strand | P26535 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.68 | 0.74 | 60 | empty |
| 2 | 1088 | 0.68 | 0.74 | 61 | empty |
| 3 | 462 | 0.67 | 0.79 | 61 | empty |
| 4 | 466 | 0.67 | 0.79 | 67 | empty |
| 5 | 371 | 0.67 | 0.80 | 64 | empty |
Interfaces
26 interfaces between chains.
- G–J · 3591 Ų buried · 53 hydrogen bonds · protein-protein
- I–J · 3559 Ų buried · 56 hydrogen bonds · protein-protein
- B–E · 3559 Ų buried · 51 hydrogen bonds · protein-protein
- F–H · 3541 Ų buried · 52 hydrogen bonds · protein-protein
- D–E · 3535 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 6IGD · Crystal structure of HPV58/33 chimeric L1 pentamer · 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 P26535
- Elsewhere: RCSB PDB 6IGD · PDBe 6IGD · UniProt P26535
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