Research workbench
Crystal structure of the SF12 Fab
Analyse Crystal structure of the SF12 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OKQ
- Type
- protein
- Length
- 1,320 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SF12 Fab heavy CHAIN,SF12 Fab heavy chain; SF12 Fab light CHAIN,SF12 Fab light chain
- UniProt
- P0DOX5, Q8TCD0
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | SF12 Fab heavy CHAIN,SF12 Fab heavy chain | protein | 230 | 8% helix, 46% strand | P0DOX5 |
| B, C, E | SF12 Fab light CHAIN,SF12 Fab light chain | protein | 210 | 6% helix, 52% strand | Q8TCD0 |
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.80 | 0.82 | 121 | empty |
| 2 | 621 | 0.78 | 0.84 | 82 | empty |
| 3 | 260 | 0.68 | 0.84 | 40 | empty |
| 4 | 183 | 0.60 | 0.82 | 30 | empty |
| 5 | 440 | 0.57 | 0.74 | 45 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1911 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1907 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1878 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 566 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 527 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6OKQ · Crystal structure of the SF12 Fab · 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
- Every structure of UniProt P0DOX5
- Every structure of UniProt Q8TCD0
- Elsewhere: RCSB PDB 6OKQ · PDBe 6OKQ · UniProt P0DOX5 · UniProt Q8TCD0
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