Research workbench
Fab of anti-a-synuclein antibody BIIB054 in complex with acetylated a- synuclein peptide (1-10)
Analyse Fab of anti-a-synuclein antibody BIIB054 in complex with acetylated a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CT7
- Type
- protein
- Length
- 865 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BIIB054 Fab light chain; BIIB054 Fab heavy chain…
- Ligands
- ACE
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | BIIB054 Fab light chain | protein | 212 | 7% helix, 49% strand | — |
| H | BIIB054 Fab heavy chain | protein | 214 | 10% helix, 50% strand | — |
| S, T | ACE-met-asp-val-phe-met-lys-gly-leu-ser-lys | protein | 10 | 0% helix, 0% strand | — |
| B | BIIB054 Fab light chain | protein | 211 | 7% helix, 49% strand | — |
| A | BIIB054 Fab heavy chain | protein | 208 | 11% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains L, H, S, B, A, T
- IPA · Isopropyl alcohol · additive · 4 copies · chains L, H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.75 | 0.83 | 60 | IPA |
| 2 | 51 | 0.70 | 0.98 | 25 | empty |
| 3 | 151 | 0.59 | 0.83 | 24 | empty |
| 4 | 130 | 0.58 | 0.84 | 18 | empty |
| 5 | 162 | 0.53 | 0.80 | 25 | empty |
Interfaces
12 interfaces between chains.
- B–A · 1543 Ų buried · 11 hydrogen bonds · protein-protein
- L–H · 1542 Ų buried · 19 hydrogen bonds · protein-protein
- B–T · 468 Ų buried · 5 hydrogen bonds · protein-protein
- L–S · 465 Ų buried · 8 hydrogen bonds · protein-protein
- A–T · 375 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6CT7 · Fab of anti-a-synuclein antibody BIIB054 in complex with acetylated a-synuclein peptide… · the same entry in another collection · chain L against L, 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 6CT7 · PDBe 6CT7
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