Research workbench
Crystal structure of Fab fragment of anti-ciguatoxin antibody 10C9 in complex with CTX3C-abcd
Analyse Crystal structure of Fab fragment of anti-ciguatoxin antibody 10C9 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z93
- Type
- protein
- Length
- 546 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-ciguatoxin antibody 10C9 Fab heavy chain; Anti-ciguatoxin antibody 10C9 Fab light…
- Ligands
- END
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-ciguatoxin antibody 10C9 Fab heavy chain | protein | 81 | 4% helix, 57% strand | — |
| B | Anti-ciguatoxin antibody 10C9 Fab light chain | protein | 80 | 13% helix, 50% strand | — |
| C | Anti-ciguatoxin antibody 10C9 Fab heavy chain | protein | 201 | 6% helix, 52% strand | — |
| D | Anti-ciguatoxin antibody 10C9 Fab light chain | protein | 184 | 4% helix, 45% strand | — |
Ligands and binding sites
- END · 1,6:5,9:8,12:11,16-tetraanhydro-2,3,4,10,13,14-hexadeoxy-D-glycero-D-allo-D-gulo-heptadeca-2,13-dienitol · ligand · chains C, 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 | 661 | 0.65 | 0.75 | 64 | empty |
| 2 | 401 | 0.61 | 0.77 | 47 | empty |
| 3 | 153 | 0.61 | 0.84 | 23 | END |
| 4 | 75 | 0.51 | 0.85 | 24 | empty |
| 5 | 78 | 0.44 | 0.81 | 27 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1765 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 819 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 293 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 56 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2Z93 · Crystal structure of Fab fragment of anti-ciguatoxin antibody 10C9 in complex with… · 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 2Z93 · PDBe 2Z93
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