MolNFT v1 · #171191 · protein
De novo designed protein 4E1H_95 in complex with 101F antibody
6YWC · Antibody 101F, heavy chain: “De novo designed protein 4E1H_95 in complex with 101F antibody”. X-ray diffraction, 10 pockets (best druggability 0.74). MolNFT v1 #171191 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YWC
- Type
- protein
- Length
- 994 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody 101F, heavy chain; Antibody 101F, light chain; De novo design 4E1H_95
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Antibody 101F, heavy chain | protein | 221 | 11% helix, 52% strand | — |
| B | Antibody 101F, light chain | protein | 218 | 6% helix, 54% strand | — |
| C, F | De novo design 4E1H_95 | protein | 58 | 24% helix, 45% strand | — |
| E | Antibody 101F, light chain | protein | 218 | 6% helix, 52% strand | — |
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.74 | 0.77 | 111 | empty |
| 2 | 621 | 0.64 | 0.75 | 47 | empty |
| 3 | 197 | 0.49 | 0.76 | 26 | empty |
| 4 | 72 | 0.45 | 0.81 | 15 | empty |
| 5 | 139 | 0.41 | 0.74 | 20 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2128 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2031 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 672 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 587 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 572 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6YWC · De novo designed protein 4E1H_95 in complex with 101F antibody · 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
- Elsewhere: RCSB PDB 6YWC · PDBe 6YWC
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