MolNFT v2 · #223285 · protein + RNA
The crystal structure of rhinovirus C15 RNA replication element sD-loop mutant in complex with Fab BL3-6
8VMA · Heavy Chain of Fab BL3-6: “The crystal structure of rhinovirus C15 RNA replication element sD-loop mutant in complex with Fab BL3-6”. X-ray diffraction at 2.54, 15 pockets (best druggability 0.82). MolNFT v2 #223285 on GenesisL1: 3D…
- PDB
- 8VMA
- Type
- protein + RNA
- Length
- 1,056 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.54
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Heavy Chain of Fab BL3-6; Light Chain of Fab BL3-6; RNA (88-mer)
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.54 · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Heavy Chain of Fab BL3-6 | protein | 225 | 10% helix, 50% strand | — |
| B, L | Light Chain of Fab BL3-6 | protein | 215 | 6% helix, 51% strand | — |
| C, R | RNA (88-mer) | rna | 88 | — | — |
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.82 | 0.83 | 117 | empty |
| 2 | 918 | 0.67 | 0.74 | 68 | empty |
| 3 | 882 | 0.65 | 0.73 | 42 | empty |
| 4 | 799 | 0.65 | 0.74 | 59 | empty |
| 5 | 807 | 0.64 | 0.74 | 35 | empty |
Interfaces
14 interfaces between chains.
- H–L · 2031 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1988 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 670 Ų buried · 15 hydrogen bonds · protein-nucleic
- H–R · 634 Ų buried · 12 hydrogen bonds · protein-nucleic
- L–C · 307 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide (disulfide).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 8VMA · PDBe 8VMA
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