MolNFT v1 · #22494 · protein
Crystal structure analysis of the nurse shark new antigen receptor (nar) variable domain in complex with lysozyme
1T6V · Lysozyme C: “Crystal structure analysis of the nurse shark new antigen receptor (nar) variable domain in complex with…”. X-ray diffraction, 1 ligand (CL), 2 pockets (best druggability 0.77). MolNFT v1 #22494 on GenesisL1: 3D…
- 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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