Research workbench
A structural basis for selection and cross-species reactivity of the semi-invariant nkt cell receptor in CD1D/GLYCOLIPID recognition
Analyse A structural basis for selection and cross-species reactivity of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EYS
- Type
- protein
- Length
- 445 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NKT15
- UniProt
- Q6PIZ8, Q6GMR4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NKT15 | protein | 202 | 3% helix, 46% strand | Q6PIZ8 |
| B | NKT15 | protein | 243 | 7% helix, 49% strand | Q6GMR4 |
Ligands and binding sites
- ACY · Acetic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.72 | 0.77 | 86 | empty |
| 2 | 115 | 0.42 | 0.77 | 20 | empty |
| 3 | 64 | 0.30 | 0.74 | 15 | empty |
| 4 | 55 | 0.28 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2248 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2EYS · A structural basis for selection and cross-species reactivity of the semi-invariant NKT… · 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 Q6PIZ8
- Every structure of UniProt Q6GMR4
- Elsewhere: RCSB PDB 2EYS · PDBe 2EYS · UniProt Q6PIZ8 · UniProt Q6GMR4
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