Research workbench
Crystal structure of HLA-DR4 bound to GP100 peptide
Analyse Crystal structure of HLA-DR4 bound to GP100 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IS6
- Type
- protein
- Length
- 380 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
- UniProt
- P01903, P13760, P40967
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 13% helix, 46% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 188 | 17% helix, 44% strand | P13760 |
| C | Melanocyte protein pmel | protein | 13 | 0% helix, 8% strand | P40967 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.48 | 0.75 | 25 | empty |
| 2 | 106 | 0.37 | 0.75 | 17 | empty |
| 3 | 57 | 0.27 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2519 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 728 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 654 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4IS6 · Crystal structure of HLA-DR4 bound to GP100 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.96
- P40967 · AlphaFold monomer V2.0 prediction for melanocyte protein pmel (P40967) · a predicted model of the same protein · chain C against A, TM-score 0.39
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 P01903
- Every structure of UniProt P13760
- Every structure of UniProt P40967
- Elsewhere: RCSB PDB 4IS6 · PDBe 4IS6 · UniProt P01903 · UniProt P13760 · UniProt P40967
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