Research workbench
Crystal structure analysis of the nurse shark new antigen receptor (nar) variable domain in complex with lysozyme
Analyse Crystal structure analysis of the nurse shark new antigen receptor (nar)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T6V
- Type
- protein
- Length
- 482 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme C; Novel antigen receptor
- EC
- 3.2.1.17
- UniProt
- P00698, Q8AXI4
- Ligands
- CL
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Lysozyme C (EC 3.2.1.17) | protein | 129 | 40% helix, 11% strand | P00698 |
| N, O | Novel antigen receptor | protein | 112 | 7% helix, 47% strand | Q8AXI4 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains N, O
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 | 1188 | 0.77 | 0.79 | 94 | empty |
| 2 | 75 | 0.30 | 0.73 | 18 | empty |
Interfaces
5 interfaces between chains.
- L–N · 826 Ų buried · 16 hydrogen bonds · protein-protein
- M–O · 765 Ų buried · 14 hydrogen bonds · protein-protein
- L–M · 310 Ų buried · 1 hydrogen bond · protein-protein
- N–M · 146 Ų buried · 1 hydrogen bond · protein-protein
- N–O · 122 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1T6V · Crystal structure analysis of the nurse shark new antigen receptor (NAR) variable domain… · the same entry in another collection · chain L against L, 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
- Every structure of UniProt Q8AXI4
- Elsewhere: RCSB PDB 1T6V · PDBe 1T6V · UniProt P00698 · UniProt Q8AXI4
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