Research workbench
Protein complex
Analyse Protein complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GG6
- Type
- protein
- Length
- 1,573 residues
- Chains
- 10
- 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, P01920, P18573
- Ligands
- NAG
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dq alpha 1 chain | protein | 180 | 15% helix, 44% strand | P01909 |
| B | HLA class II histocompatibility antigen, dq beta 1 chain | protein | 163 | 21% helix, 42% strand | P01920 |
| C | HLA class II histocompatibility antigen, dq alpha 1 chain | protein | 181 | 15% helix, 44% strand | P01909 |
| D | HLA class II histocompatibility antigen, dq beta 1 chain | protein | 173 | 20% helix, 43% strand | P01920 |
| E | T-cell receptor, SP3.4 alpha chain | protein | 187 | 2% helix, 42% strand | — |
| F, H | T-cell receptor, SP3.4 beta chain | protein | 243 | 7% helix, 51% strand | — |
| G | T-cell receptor, SP3.4 alpha chain | protein | 177 | 2% helix, 44% strand | — |
| I, J | Peptide from ALPHA/BETA-gliadin MM1 | protein | 13 | 0% helix, 8% strand | P18573 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.75 | 0.77 | 80 | empty |
| 2 | 1041 | 0.73 | 0.77 | 95 | empty |
| 3 | 920 | 0.69 | 0.74 | 74 | empty |
| 4 | 106 | 0.59 | 0.85 | 21 | empty |
| 5 | 115 | 0.47 | 0.79 | 38 | empty |
Interfaces
23 interfaces between chains.
- A–B · 2650 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 2642 Ų buried · 60 hydrogen bonds · protein-protein
- E–F · 2161 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 2102 Ų buried · 39 hydrogen bonds · protein-protein
- B–J · 714 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4GG6 · Protein complex · the same entry in another collection · chain J against J, TM-score 1.00
- P01920 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dq beta 1… · a predicted model of the same protein · chain D against A, TM-score 0.94
- P01909 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dq alpha 1… · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P01920
- Every structure of UniProt P18573
- Elsewhere: RCSB PDB 4GG6 · PDBe 4GG6 · UniProt P01909 · UniProt P01920 · UniProt P18573
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