Research workbench
Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I
Analyse Crystal structure of human paired immunoglobulin-like type 2 receptor alpha… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XOF
- Type
- protein
- Length
- 507 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Paired immunoglobulin-like type 2 receptor alpha; Peptide from nitric oxide synthase…
- EC
- 1.14.13.39
- UniProt
- Q9UKJ1, P29474
- Ligands
- NDG, SIA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Paired immunoglobulin-like type 2 receptor alpha | protein | 119 | 3% helix, 50% strand | Q9UKJ1 |
| B, C, D | Paired immunoglobulin-like type 2 receptor alpha | protein | 120 | 3% helix, 51% strand | Q9UKJ1 |
| O, P, Q, R | Peptide from nitric oxide synthase, endothelial (EC 1.14.13.39) | protein | 7 | 0% helix, 0% strand | P29474 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 4 copies · chains A, C, O, B, D, P, Q, R
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains A, O, B, P, C, Q, D, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.80 | 0.82 | 110 | empty |
| 2 | 107 | 0.45 | 0.78 | 22 | empty |
| 3 | 172 | 0.44 | 0.74 | 26 | empty |
| 4 | 87 | 0.35 | 0.75 | 19 | SIA |
| 5 | 71 | 0.33 | 0.75 | 20 | SIA |
Interfaces
12 interfaces between chains.
- C–Q · 248 Ų buried · 1 hydrogen bond · protein-protein
- D–R · 248 Ų buried · 1 hydrogen bond · protein-protein
- B–P · 242 Ų buried · 1 hydrogen bond · protein-protein
- A–O · 236 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 235 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (O-glycosylation).
Compared structures
- 5XOF · Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with… · the same entry in another collection · chain R against R, TM-score 1.00
- Q9UKJ1 · AlphaFold monomer V2.0 prediction for paired immunoglobulin-like type 2 receptor alpha… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9UKJ1
- Every structure of UniProt P29474
- Elsewhere: RCSB PDB 5XOF · PDBe 5XOF · UniProt Q9UKJ1 · UniProt P29474
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