Research workbench
Crystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme
Analyse Crystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JB2
- Type
- protein
- Length
- 255 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Camelus dromedarius; Gallus gallus
- Molecule
- Nanobody D3-L11; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Ligands
- CL
- Pockets
- 1 · best druggability 0.49
Structure
x-ray diffraction · resolution 1.5 · 2 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody D3-L11 | protein | 126 | 14% helix, 50% strand | — |
| B | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.49 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 741 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6JB2 · Crystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme · 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
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 6JB2 · PDBe 6JB2 · UniProt P00698
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