Research workbench
Crystal structure of an immune complex at pH 6.5
Analyse Crystal structure of an immune complex at pH 6.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GBX
- Type
- protein
- Length
- 759 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dm alpha chain; HLA class II histocompatibility…
- UniProt
- P28067, P28068, P01903, P04229
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | HLA class II histocompatibility antigen, dm alpha chain | protein | 189 | 12% helix, 49% strand | P28067 |
| D | HLA class II histocompatibility antigen, dm beta chain | protein | 191 | 18% helix, 38% strand | P28068 |
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 16% helix, 44% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 189 | 20% helix, 46% strand | P04229 |
| E | Synthetic peptide | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C, D, A, B
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 | 1174 | 0.76 | 0.78 | 108 | empty |
| 2 | 166 | 0.66 | 0.87 | 25 | empty |
| 3 | 230 | 0.53 | 0.76 | 40 | empty |
| 4 | 162 | 0.46 | 0.76 | 32 | empty |
| 5 | 126 | 0.43 | 0.76 | 20 | empty |
Interfaces
7 interfaces between chains.
- C–D · 2750 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2615 Ų buried · 43 hydrogen bonds · protein-protein
- C–A · 1111 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 514 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 460 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4GBX · Crystal structure of an immune complex at pH 6.5 · the same entry in another collection · chain E against E, TM-score 1.00
- P28067 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dm alpha… · a predicted model of the same protein · chain C against A, TM-score 0.98
- P28068 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dm beta… · a predicted model of the same protein · chain D against A, TM-score 0.93
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P28067
- Every structure of UniProt P28068
- Every structure of UniProt P01903
- Every structure of UniProt P04229
- Elsewhere: RCSB PDB 4GBX · PDBe 4GBX · UniProt P28067 · UniProt P28068 · UniProt P01903 · UniProt P04229
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