Research workbench
Murine Fab that recognizes hev B 8 (profilin for hevea brasiliensis)
Analyse Murine Fab that recognizes hev B 8 (profilin for hevea brasiliensis) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SD2
- Type
- protein
- Length
- 1,231 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain antibody IGE/FAB anti-profilin hev B 8; Light chain antibody IGE/FAB…
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain antibody IGE/FAB anti-profilin hev B 8 | protein | 204 | 1% helix, 51% strand | — |
| L, B | Light chain antibody IGE/FAB anti-profilin hev B 8 | protein | 210 | 5% helix, 50% strand | — |
| A | Heavy chain antibody IGE/FAB anti-profilin hev B 8 | protein | 201 | 1% helix, 48% strand | — |
| C | Heavy chain antibody IGE/FAB anti-profilin hev B 8 | protein | 197 | 2% helix, 49% strand | — |
| D | Light chain antibody IGE/FAB anti-profilin hev B 8 | protein | 209 | 6% helix, 50% strand | — |
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.81 | 0.82 | 75 | empty |
| 2 | 198 | 0.74 | 0.90 | 40 | empty |
| 3 | 765 | 0.71 | 0.77 | 109 | empty |
| 4 | 222 | 0.70 | 0.87 | 34 | empty |
| 5 | 498 | 0.61 | 0.75 | 49 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1414 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 1400 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1266 Ų buried · 2 hydrogen bonds · protein-protein
- H–D · 457 Ų buried · 9 hydrogen bonds · protein-protein
- L–A · 326 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7SD2 · Murine Fab that recognizes Hev b 8 (profilin for Hevea brasiliensis) · 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 7SD2 · PDBe 7SD2
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