Research workbench
X-ray crystal structure of HLA-DR4 complexed with peptidomimetic and seb
Analyse X-ray crystal structure of HLA-DR4 complexed with peptidomimetic and seb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D5Z
- Type
- protein
- Length
- 591 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (HLA class II histocompatibility antigen); Protein (enterotoxin type B); Protein…
- UniProt
- P01903, P13760, P01552
- Ligands
- ACE, NH2
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (HLA class II histocompatibility antigen) | protein | 178 | 13% helix, 47% strand | P01903 |
| B | Protein (HLA class II histocompatibility antigen) | protein | 181 | 20% helix, 46% strand | P13760 |
| C | Protein (enterotoxin type B) | protein | 226 | 19% helix, 40% strand | P01552 |
| D | Protein (peptidomimetic inhibitor) | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 211 | 0.49 | 0.75 | 25 | empty |
| 2 | 127 | 0.40 | 0.75 | 19 | empty |
| 3 | 79 | 0.32 | 0.74 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2541 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 777 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 520 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 377 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified, 1 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 1D5Z · X-ray crystal structure of HLA-DR4 complexed with peptidomimetic 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 0.96
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 1D5Z · PDBe 1D5Z · UniProt P01903 · UniProt P13760 · UniProt P01552
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