Research workbench
Structure of single domain antibody SD83
Analyse Structure of single domain antibody SD83 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FYS
- Type
- protein
- Length
- 1,009 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single domain antibody SD83
- Pockets
- 10 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, D, F, G, H | Single domain antibody SD83 | protein | 127 | 13% helix, 45% strand | — |
| A | Single domain antibody SD83 | protein | 126 | 7% helix, 44% strand | — |
| E | Single domain antibody SD83 | protein | 121 | 8% helix, 49% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.59 | 0.77 | 53 | empty |
| 2 | 478 | 0.58 | 0.73 | 37 | empty |
| 3 | 295 | 0.56 | 0.77 | 53 | empty |
| 4 | 119 | 0.55 | 0.83 | 24 | empty |
| 5 | 196 | 0.49 | 0.76 | 36 | empty |
Interfaces
13 interfaces between chains.
- A–H · 617 Ų buried · 7 hydrogen bonds · protein-protein
- C–G · 599 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 562 Ų buried · 13 hydrogen bonds · protein-protein
- C–B · 547 Ų buried · 11 hydrogen bonds · protein-protein
- C–A · 527 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6FYS · Structure of single domain antibody SD83 · the same entry in another collection · chain C against C, 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
- Elsewhere: RCSB PDB 6FYS · PDBe 6FYS
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