Research workbench
Crystal structure of anti-polysialic acid antibody single chain fv fragment (MAB735) complexed with octasialic acid
Analyse Crystal structure of anti-polysialic acid antibody single chain fv fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WBD
- Type
- protein
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single chain fv fragment of MAB735
- Ligands
- SIA
- Pockets
- 6 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single chain fv fragment of MAB735 | protein | 231 | 5% helix, 51% strand | — |
| B | Single chain fv fragment of MAB735 | protein | 230 | 5% helix, 52% strand | — |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 7 copies · chains B, A
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.31 | 0.76 | 15 | empty |
| 2 | 64 | 0.31 | 0.75 | 17 | empty |
| 3 | 65 | 0.30 | 0.74 | 17 | empty |
| 4 | 54 | 0.30 | 0.76 | 13 | empty |
| 5 | 65 | 0.30 | 0.74 | 16 | SIA |
Interfaces
1 interface between chains.
- A–B · 226 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3WBD · Crystal structure of anti-polysialic acid antibody single chain Fv fragment (mAb735)… · 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
- Elsewhere: RCSB PDB 3WBD · PDBe 3WBD
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