Research workbench
X-ray crystal structure of HLA-DR4 complexed with dipeptide mimetic and seb
Analyse X-ray crystal structure of HLA-DR4 complexed with dipeptide mimetic and seb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D5X
- Type
- protein
- Length
- 589 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen; Enterotoxin type B; Dipeptide mimetic inhibitor
- UniProt
- P01903, P13760, P01552
- Ligands
- ACE, SEL
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen | protein | 179 | 13% helix, 46% strand | P01903 |
| B | HLA class II histocompatibility antigen | protein | 183 | 17% helix, 43% strand | P13760 |
| C | Enterotoxin type B | protein | 223 | 20% helix, 40% strand | P01552 |
| D | Dipeptide mimetic inhibitor | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 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 | 29 | empty |
| 2 | 122 | 0.43 | 0.77 | 25 | empty |
| 3 | 67 | 0.35 | 0.77 | 14 | SEL |
| 4 | 52 | 0.25 | 0.72 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2534 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 761 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 402 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 279 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 modified, 2 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 1D5X · X-ray crystal structure of HLA-DR4 complexed with dipeptide mimetic and seb · the same entry in another collection · chain A against A, TM-score 1.00
- P01552 · AlphaFold monomer V2.0 prediction for enterotoxin type B (P01552) · a predicted model of the same protein · chain C against A, TM-score 0.99
- 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 0.95
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 P01552
- Elsewhere: RCSB PDB 1D5X · PDBe 1D5X · UniProt P01903 · UniProt P13760 · UniProt P01552
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