Research workbench
Crystal structure of the apo antibody fragment (Fab) raised against C- terminal domain of ebola nucleoprotein (ebov, tafv, bdbv strains)
Analyse Crystal structure of the apo antibody fragment (Fab) raised against C- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B6Z
- Type
- protein
- Length
- 834 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apo Fab light chain; Apo Fab heavy chain
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apo Fab light chain | protein | 200 | 6% helix, 54% strand | — |
| B | Apo Fab heavy chain | protein | 219 | 9% helix, 51% strand | — |
| C | Apo Fab light chain | protein | 198 | 6% helix, 53% strand | — |
| D | Apo Fab heavy chain | protein | 217 | 6% helix, 53% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.75 | 0.79 | 106 | empty |
| 2 | 639 | 0.72 | 0.79 | 89 | empty |
| 3 | 290 | 0.64 | 0.82 | 47 | ZN |
| 4 | 316 | 0.60 | 0.78 | 31 | empty |
| 5 | 137 | 0.48 | 0.78 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1874 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1834 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1430 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 82 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 62 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6B6Z · Crystal structure of the Apo Antibody fragment (Fab) raised against C-terminal domain of… · 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 6B6Z · PDBe 6B6Z
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