Research workbench
Structure of bovine anti-rsv Fab B13
Analyse Structure of bovine anti-rsv Fab B13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QN8
- Type
- protein
- Length
- 2,643 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of bovine anti-rsv B13 Fab; Light chain of bovine anti-rsv Fab B13
- Ligands
- CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of bovine anti-rsv B13 Fab | protein | 227 | 5% helix, 52% strand | — |
| L, B, D, F, I, K | Light chain of bovine anti-rsv Fab B13 | protein | 213 | 8% helix, 51% strand | — |
| A | Heavy chain of bovine anti-rsv B13 Fab | protein | 235 | 6% helix, 52% strand | — |
| C | Heavy chain of bovine anti-rsv B13 Fab | protein | 226 | 7% helix, 54% strand | — |
| E | Heavy chain of bovine anti-rsv B13 Fab | protein | 226 | 7% helix, 53% strand | — |
| G | Heavy chain of bovine anti-rsv B13 Fab | protein | 224 | 5% helix, 53% strand | — |
| J | Heavy chain of bovine anti-rsv B13 Fab | protein | 227 | 5% helix, 54% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains B, D, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.77 | 0.82 | 60 | empty |
| 2 | 580 | 0.77 | 0.83 | 68 | CL |
| 3 | 685 | 0.74 | 0.80 | 68 | empty |
| 4 | 903 | 0.70 | 0.76 | 78 | empty |
| 5 | 862 | 0.70 | 0.76 | 77 | empty |
Interfaces
24 interfaces between chains.
- C–D · 2103 Ų buried · 18 hydrogen bonds · protein-protein
- G–I · 2047 Ų buried · 16 hydrogen bonds · protein-protein
- J–K · 2036 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 2005 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1987 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 6QN8 · Structure of bovine anti-RSV Fab B13 · the same entry in another collection · chain C against C, 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 6QN8 · PDBe 6QN8
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