Research workbench
Structure of the 093G9 Fab in complex with the epitope peptide
Analyse Structure of the 093G9 Fab in complex with the epitope peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WTT
- Type
- protein
- Length
- 878 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of 093G9 Fab; Light chain of 093G9 Fab; Epitope peptide of CYR61
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of 093G9 Fab | protein | 214 | 3% helix, 52% strand | — |
| L, B | Light chain of 093G9 Fab | protein | 216 | 5% helix, 51% strand | — |
| P, C | Epitope peptide of CYR61 | protein | 8 | 63% helix, 0% strand | — |
| A | Heavy chain of 093G9 Fab | protein | 216 | 3% helix, 52% strand | — |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.65 | 0.81 | 44 | empty |
| 2 | 242 | 0.51 | 0.75 | 42 | empty |
| 3 | 221 | 0.49 | 0.75 | 39 | empty |
| 4 | 111 | 0.39 | 0.75 | 25 | empty |
| 5 | 97 | 0.37 | 0.75 | 22 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1883 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 1872 Ų buried · 16 hydrogen bonds · protein-protein
- H–P · 359 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 356 Ų buried · 4 hydrogen bonds · protein-protein
- L–P · 317 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5WTT · Structure of the 093G9 Fab in complex with the epitope peptide · the same entry in another collection · chain H against H, 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 5WTT · PDBe 5WTT
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