Research workbench
Crystal structure of the camelid single domain antibody 1D2L19 in complex with hen egg white lysozyme
Analyse Crystal structure of the camelid single domain antibody 1D2L19 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RI8
- Type
- protein
- Length
- 253 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camelid antibody heavy chain; Lysozyme C
- EC
- 3.2.1.17
- UniProt
- P00698
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camelid antibody heavy chain | protein | 124 | 7% helix, 56% strand | — |
| B | Lysozyme C (EC 3.2.1.17) | protein | 129 | 41% helix, 12% strand | P00698 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.51 | 0.78 | 24 | GOL |
| 2 | 173 | 0.49 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 741 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1RI8 · Crystal Structure of the Camelid Single Domain Antibody 1D2L19 in complex with Hen Egg… · 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 1RI8 · PDBe 1RI8 · UniProt P00698
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