Research workbench
Crystal structure of a nanobody raised against KDM5B
Analyse Crystal structure of a nanobody raised against KDM5B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZG1
- Type
- protein
- Length
- 701 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NB17
- Pockets
- 8 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F | NB17 | protein | 117 | 5% helix, 55% strand | — |
| D | NB17 | protein | 116 | 8% helix, 53% strand | — |
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.89 | 0.92 | 118 | empty |
| 2 | 82 | 0.75 | 0.97 | 19 | empty |
| 3 | 79 | 0.74 | 0.97 | 19 | empty |
| 4 | 67 | 0.73 | 0.98 | 18 | empty |
| 5 | 70 | 0.73 | 0.97 | 21 | empty |
Interfaces
13 interfaces between chains.
- B–C · 577 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 565 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 490 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 433 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 403 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4ZG1 · PDBe 4ZG1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.