Research workbench
Crystal structure of the mirror-image L-RNA/L-DNA aptamer nox-D20 in complex with mouse C5A-desarg complement anaphylatoxin
Analyse Crystal structure of the mirror-image L-RNA/L-DNA aptamer nox-D20 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WB3
- Type
- protein + RNA
- Length
- 285 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement C5; Mixed L-RNA/L-DNA aptamer nox-D20 (40-mer)
- UniProt
- P06684
- Ligands
- CA, MG
- Pockets
- 12 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C5 | protein | 68 | 71% helix, 0% strand | P06684 |
| B | Complement C5 | protein | 68 | 66% helix, 0% strand | P06684 |
| C | Complement C5 | protein | 69 | 67% helix, 0% strand | P06684 |
| D, E | Mixed L-RNA/L-DNA aptamer nox-D20 (40-mer) | rna | 40 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, D, C, E
- MG · Magnesium ion · metal · 2 copies · chains D, E
- ACT · Acetate ion · additive · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.63 | 0.83 | 30 | CA |
| 2 | 80 | 0.51 | 0.85 | 11 | ACT |
| 3 | 62 | 0.50 | 0.86 | 19 | CA |
| 4 | 162 | 0.50 | 0.78 | 16 | empty |
| 5 | 73 | 0.49 | 0.85 | 10 | empty |
Interfaces
5 interfaces between chains.
- A–D · 924 Ų buried · 28 hydrogen bonds · protein-nucleic
- C–E · 852 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 500 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 196 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- B–D · 91 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 80 modified, 9 disulfide (nucleotide modification, disulfide).
Compared structures
- 4WB3 · Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse… · the same entry in another collection · chain E against E, TM-score 1.00
- P06684 · AlphaFold monomer V2.0 prediction for complement C5 (P06684) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P06684
- Elsewhere: RCSB PDB 4WB3 · PDBe 4WB3 · UniProt P06684
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