Research workbench
L3-12 complex
Analyse L3-12 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z7V
- Type
- protein
- Length
- 1,615 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II HLA-dq-alpha chain; MHC class II HLA-dq-beta-1; T-cell receptor, L3-12 alpha…
- UniProt
- Q30069, O19707
- Ligands
- NAG, FUC, MAN
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | MHC class II HLA-dq-alpha chain | protein | 180 | 15% helix, 44% strand | Q30069 |
| B | MHC class II HLA-dq-beta-1 | protein | 172 | 21% helix, 43% strand | O19707 |
| D | MHC class II HLA-dq-beta-1 | protein | 175 | 21% helix, 40% strand | O19707 |
| E | T-cell receptor, L3-12 alpha chain | protein | 199 | 5% helix, 46% strand | — |
| F | T-cell receptor, L3-12 beta chain | protein | 243 | 7% helix, 51% strand | — |
| G | T-cell receptor, L3-12 alpha chain | protein | 198 | 3% helix, 46% strand | — |
| H | T-cell receptor, L3-12 beta chain | protein | 242 | 7% helix, 51% strand | — |
| I, J | Deamidated DQ8-glia-ALPHA1 peptide | protein | 13 | 0% helix, 8% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, D, A, C
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, D
- MAN · alpha-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.70 | 0.75 | 82 | empty |
| 2 | 972 | 0.69 | 0.74 | 78 | empty |
| 3 | 270 | 0.53 | 0.75 | 35 | empty |
| 4 | 209 | 0.46 | 0.74 | 33 | empty |
| 5 | 165 | 0.45 | 0.76 | 36 | empty |
Interfaces
25 interfaces between chains.
- A–B · 2561 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 2560 Ų buried · 57 hydrogen bonds · protein-protein
- E–F · 2069 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 2063 Ų buried · 29 hydrogen bonds · protein-protein
- B–J · 718 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4Z7V · L3-12 complex · the same entry in another collection · chain C against C, 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 Q30069
- Every structure of UniProt O19707
- Elsewhere: RCSB PDB 4Z7V · PDBe 4Z7V · UniProt Q30069 · UniProt O19707
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