MolNFT v1 · #21662 · protein
Convergent solutions to vhh domain stabilization from natural and in vitro evolution
1SHM · Antibody rig: “Convergent solutions to vhh domain stabilization from natural and in vitro evolution”. X-ray diffraction, 3 pockets (best druggability 0.73). MolNFT v1 #21662 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1SHM
- Type
- protein
- Length
- 466 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody rig
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Antibody rig | protein | 118 | 5% helix, 53% strand | — |
| B | Antibody rig | protein | 117 | 3% helix, 54% strand | — |
| D | Antibody rig | protein | 113 | 5% helix, 54% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.73 | 0.77 | 91 | empty |
| 2 | 68 | 0.53 | 0.86 | 18 | empty |
| 3 | 77 | 0.45 | 0.81 | 13 | empty |
Interfaces
4 interfaces between chains.
- B–E · 536 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 485 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 424 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 264 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1SHM · Convergent solutions to VHH domain stabilization from natural and in vitro evolution · the same entry in another collection · chain D against D, 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 1SHM · PDBe 1SHM
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