Research workbench
Predicting amino acid preferences in the complementarity determining regions of an antibody-antigen recognition interface
Analyse Predicting amino acid preferences in the complementarity determining regions of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AUV
- Type
- protein
- Length
- 1,351 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sc-dsfv derived from the G6-Fab
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sc-dsfv derived from the G6-Fab | protein | 225 | 7% helix, 48% strand | — |
| B, C, E | Sc-dsfv derived from the G6-Fab | protein | 225 | 7% helix, 48% strand | — |
| D | Sc-dsfv derived from the G6-Fab | protein | 227 | 7% helix, 49% strand | — |
| F | Sc-dsfv derived from the G6-Fab | protein | 224 | 7% helix, 48% strand | — |
Pockets
16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.79 | 0.82 | 140 | empty |
| 2 | 206 | 0.54 | 0.78 | 30 | empty |
| 3 | 195 | 0.53 | 0.78 | 27 | empty |
| 4 | 157 | 0.46 | 0.75 | 28 | empty |
| 5 | 132 | 0.44 | 0.76 | 28 | empty |
Interfaces
9 interfaces between chains.
- D–F · 792 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 792 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 788 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 785 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 782 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 3AUV · Predicting Amino Acid Preferences in the Complementarity Determining Regions of an… · 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 3AUV · PDBe 3AUV
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