MolNFT v1 · #117793 · protein
Crystal structure of complex of osteoclast-associated immunoglobulin- like receptor (oscar) and a synthetic collagen consensus peptide
5EIV · Osteoclast-associated immunoglobulin-like receptor: “Crystal structure of complex of osteoclast-associated immunoglobulin- like receptor (oscar) and a synthetic…”. X-ray diffraction, 4 ligands (NAG, NA, SO4), 1 pocket (best…
- PDB
- 5EIV
- Type
- protein
- Length
- 504 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Osteoclast-associated immunoglobulin-like receptor…
- UniProt
- Q8IYS5
- Ligands
- NAG, NA, SO4, CL
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 7 distinct chains · 3% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Osteoclast-associated immunoglobulin-like receptor | protein | 181 | 3% helix, 48% strand | Q8IYS5 |
| B | Osteoclast-associated immunoglobulin-like receptor | protein | 181 | 3% helix, 45% strand | Q8IYS5 |
| C, E, H | Gly-pro-hyp-gly-pro-hyp-gly-pro-hyp-gly-pro-ala-gly-phe- hyp-gly-pro-hyp-gly-pro-hyp | protein | 21 | 0% helix, 0% strand | — |
| D, G | Gly-pro-hyp-gly-pro-hyp-gly-pro-hyp-gly-pro-ala-gly-phe- hyp-gly-pro-hyp-gly-pro-hyp | protein | 20 | 0% helix, 0% strand | — |
| F | Gly-pro-hyp-gly-pro-hyp-gly-pro-hyp-gly-pro-ala-gly-phe- hyp-gly-pro-hyp-gly-pro-hyp | protein | 20 | 0% helix, 0% strand | — |
| I, K | Pro-gly-pro-pro-gly-pro-pro | protein | 6 | 0% helix, 0% strand | — |
| J | Pro-gly-pro-pro-gly-pro-pro | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B, C
- NA · Sodium ion · metal · 2 copies · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains A, D, E, B, F, H
- CL · Chloride ion · ion · 3 copies · chains A, F
- ACT · Acetate ion · additive · chains F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.57 | 0.74 | 50 | SO4 |
Interfaces
23 interfaces between chains.
- C–D · 655 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 645 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 623 Ų buried · 6 hydrogen bonds · protein-protein
- F–G · 621 Ų buried · 6 hydrogen bonds · protein-protein
- F–H · 609 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified, 4 disulfide, 2 glycan, 1 covalent (hydroxylation, disulfide, N-glycosylation, additive adduct).
Compared structures
- 5EIV · Crystal structure of complex of osteoclast-associated immunoglobulin-like receptor… · the same entry in another collection · chain K against K, TM-score 1.00
- Q8IYS5 · AlphaFold monomer V2.0 prediction for osteoclast-associated immunoglobulin-like receptor… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q8IYS5
- Elsewhere: RCSB PDB 5EIV · PDBe 5EIV · UniProt Q8IYS5
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