Research workbench
Crystal structure of the nod sirpa complex with D4-2
Analyse Crystal structure of the nod sirpa complex with D4-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LYC
- Type
- protein
- Length
- 125 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sirpa of the nod mouse strain; D4-2
- Ligands
- NH2
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sirpa of the nod mouse strain | protein | 110 | 8% helix, 43% strand | — |
| B | D4-2 | protein | 15 | 0% helix, 40% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 1040 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 d-amino, 1 disulfide (additive adduct, D-amino acid, disulfide).
Compared structures
- 6LYC · Crystal structure of the NOD SIRPa complex with D4-2 · 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
- Elsewhere: RCSB PDB 6LYC · PDBe 6LYC
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