MolNFT v1 · #64897 · protein
Crystal structure of Fab F22-4 in complex with a carbohydrate-mimetic peptide
3GGW · Fab F22-4 light chain: “Crystal structure of Fab F22-4 in complex with a carbohydrate-mimetic peptide”. X-ray diffraction, 13 pockets (best druggability 0.61). MolNFT v1 #64897 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3GGW
- Type
- protein
- Length
- 876 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab F22-4 light chain; Fab F22-4 heavy chain; Peptide B1
- Pockets
- 13 · best druggability 0.61
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab F22-4 light chain | protein | 218 | 6% helix, 49% strand | — |
| B | Fab F22-4 heavy chain | protein | 207 | 12% helix, 54% strand | — |
| C | Fab F22-4 light chain | protein | 219 | 5% helix, 48% strand | — |
| D | Fab F22-4 heavy chain | protein | 209 | 10% helix, 53% strand | — |
| E | Peptide B1 | protein | 11 | 82% helix, 0% strand | — |
| F | Peptide B1 | protein | 12 | 83% helix, 0% strand | — |
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.61 | 0.78 | 49 | empty |
| 2 | 163 | 0.58 | 0.82 | 38 | empty |
| 3 | 314 | 0.53 | 0.74 | 49 | empty |
| 4 | 250 | 0.50 | 0.74 | 43 | empty |
| 5 | 220 | 0.45 | 0.73 | 26 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1707 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1532 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 393 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 357 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 348 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3GGW · Crystal Structure of FAB F22-4 in complex with a Carbohydrate-mimetic peptide · the same entry in another collection · chain C against C, 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 3GGW · PDBe 3GGW
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