Research workbench
HRV14 3C in complex with single chain antibody ydf
Analyse HRV14 3C in complex with single chain antibody ydf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KYZ
- Type
- protein
- Length
- 824 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; Ydf H chain; Ydf L chain
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- P03303
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 180 | 12% helix, 58% strand | P03303 |
| B, E | Ydf H chain | protein | 127 | 5% helix, 54% strand | — |
| C, F | Ydf L chain | protein | 107 | 6% helix, 52% strand | — |
| D | Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 176 | 11% helix, 60% strand | P03303 |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.64 | 0.77 | 48 | empty |
| 2 | 442 | 0.63 | 0.78 | 49 | empty |
| 3 | 58 | 0.52 | 0.87 | 18 | empty |
| 4 | 92 | 0.47 | 0.81 | 18 | empty |
| 5 | 109 | 0.44 | 0.77 | 21 | empty |
Interfaces
9 interfaces between chains.
- E–F · 805 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 765 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 513 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 500 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 490 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6KYZ · HRV14 3C in complex with single chain antibody YDF · 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 P03303
- Elsewhere: RCSB PDB 6KYZ · PDBe 6KYZ · UniProt P03303
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