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
- 5VZ1
- Type
- protein
- Length
- 827 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apo antibody Fab light chain; Apo antibody Fab heavy chain
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apo antibody Fab light chain | protein | 200 | 5% helix, 54% strand | — |
| B | Apo antibody Fab heavy chain | protein | 217 | 8% helix, 52% strand | — |
| C | Apo antibody Fab light chain | protein | 196 | 7% helix, 53% strand | — |
| D | Apo antibody Fab heavy chain | protein | 214 | 6% helix, 54% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B, 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 | 838 | 0.75 | 0.80 | 110 | empty |
| 2 | 713 | 0.74 | 0.80 | 95 | empty |
| 3 | 382 | 0.63 | 0.78 | 42 | empty |
| 4 | 246 | 0.59 | 0.80 | 38 | empty |
| 5 | 80 | 0.42 | 0.80 | 17 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1824 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1718 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1428 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 81 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
- 5VZ1 · 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 5VZ1 · PDBe 5VZ1
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