MolNFT v1 · #158744 · protein
Crystal structure of frizzled 7 crd in complex with F6 Fab
6O3B · Antibody Fab F6, light chain: “Crystal structure of frizzled 7 crd in complex with F6 Fab”. X-ray diffraction, 1 ligand (NAG), 13 pockets (best druggability 0.62). MolNFT v1 #158744 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6O3B
- Type
- protein
- Length
- 1,108 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab F6, light chain; Antibody Fab F6, heavy chain; Frizzled-7
- UniProt
- O75084
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Antibody Fab F6, light chain | protein | 213 | 6% helix, 52% strand | — |
| B, G | Antibody Fab F6, heavy chain | protein | 216 | 7% helix, 52% strand | — |
| C | Frizzled-7 | protein | 126 | 41% helix, 7% strand | O75084 |
| H | Frizzled-7 | protein | 124 | 43% helix, 6% strand | O75084 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, H
- GOL · Glycerol · additive · 5 copies · chains A, B, G, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.62 | 0.74 | 71 | empty |
| 2 | 570 | 0.61 | 0.74 | 58 | empty |
| 3 | 406 | 0.60 | 0.76 | 43 | GOL |
| 4 | 58 | 0.58 | 0.90 | 21 | empty |
| 5 | 310 | 0.55 | 0.75 | 32 | GOL |
Interfaces
7 interfaces between chains.
- E–G · 1793 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1728 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 857 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 832 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 613 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 O75084
- Elsewhere: RCSB PDB 6O3B · PDBe 6O3B · UniProt O75084
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