Research workbench
RTA1-33/44-198 (rvec) bound to single domain antibody A3C8
Analyse RTA1-33/44-198 (rvec) bound to single domain antibody A3C8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SV3
- Type
- protein
- Length
- 585 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-ricin a-chain single domain antibody (sdab) A3C8; Ricin
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-ricin a-chain single domain antibody (sdab) A3C8 | protein | 126 | 10% helix, 49% strand | — |
| B, D | Ricin (EC 3.2.2.22) | protein | 167 | 41% helix, 20% strand | P02879 |
| C | Anti-ricin a-chain single domain antibody (sdab) A3C8 | protein | 125 | 10% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.75 | 0.81 | 57 | empty |
| 2 | 202 | 0.58 | 0.80 | 33 | empty |
| 3 | 108 | 0.51 | 0.82 | 16 | empty |
| 4 | 288 | 0.51 | 0.74 | 24 | empty |
| 5 | 57 | 0.46 | 0.84 | 19 | empty |
Interfaces
4 interfaces between chains.
- C–D · 683 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 645 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 309 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 156 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5SV3 · RTA1-33/44-198 (RVEC) bound to Single Domain Antibody A3C8 · 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 P02879
- Elsewhere: RCSB PDB 5SV3 · PDBe 5SV3 · UniProt P02879
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