Research workbench
JR5.1 protein complex
Analyse JR5.1 protein complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OZF
- Type
- protein
- Length
- 810 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dq alpha 1 chain; HLA class II…
- UniProt
- P01909, Q5Y7D3
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dq alpha 1 chain | protein | 181 | 14% helix, 45% strand | P01909 |
| B | HLA class II histocompatibility antigen, dq beta 1 chain | protein | 181 | 19% helix, 45% strand | Q5Y7D3 |
| G | T-cell receptor, JR5.1 alpha chain | protein | 193 | 3% helix, 44% strand | — |
| H | T-cell receptor, JR5.1 beta chain | protein | 242 | 6% helix, 50% strand | — |
| J | Deamidated gliadin-ALPHA2 peptide | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.73 | 0.77 | 90 | empty |
| 2 | 122 | 0.59 | 0.85 | 28 | empty |
| 3 | 230 | 0.51 | 0.75 | 37 | empty |
| 4 | 224 | 0.50 | 0.76 | 38 | empty |
| 5 | 92 | 0.42 | 0.78 | 24 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2606 Ų buried · 52 hydrogen bonds · protein-protein
- G–H · 2140 Ų buried · 25 hydrogen bonds · protein-protein
- B–J · 682 Ų buried · 11 hydrogen bonds · protein-protein
- A–J · 661 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 363 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 P01909
- Every structure of UniProt Q5Y7D3
- Elsewhere: RCSB PDB 4OZF · PDBe 4OZF · UniProt P01909 · UniProt Q5Y7D3
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