Research workbench
Pentamer structure of major capsid protein L1 of human papilloma virus type 11
Analyse Pentamer structure of major capsid protein L1 of human papilloma virus type 11 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R5K
- Type
- protein
- Length
- 2,095 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein L1
- UniProt
- P04012
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Major capsid protein L1 | protein | 419 | 14% helix, 38% strand | P04012 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.70 | 0.74 | 54 | empty |
| 2 | 321 | 0.62 | 0.79 | 52 | empty |
| 3 | 343 | 0.61 | 0.78 | 53 | empty |
| 4 | 354 | 0.61 | 0.77 | 52 | empty |
| 5 | 281 | 0.61 | 0.79 | 51 | empty |
Interfaces
10 interfaces between chains.
- D–E · 3555 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 3550 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 3548 Ų buried · 60 hydrogen bonds · protein-protein
- A–E · 3537 Ų buried · 59 hydrogen bonds · protein-protein
- B–C · 3531 Ų buried · 60 hydrogen bonds · protein-protein
Compared structures
- 2R5K · Pentamer Structure of Major Capsid protein L1 of Human Papilloma Virus type 11 · 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 P04012
- Elsewhere: RCSB PDB 2R5K · PDBe 2R5K · UniProt P04012
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