Research workbench
X-ray crystal structure of HLA-DR4 complexed with a peptide from human collagen II
Analyse X-ray crystal structure of HLA-DR4 complexed with a peptide from human collagen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2SEB
- Type
- protein
- Length
- 586 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen; Enterotoxin type B; Peptide from collagen II
- UniProt
- P01903, P13760, P01552, P02458
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.49
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 | 180 | 14% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen | protein | 177 | 19% helix, 45% strand | P13760 |
| D | Enterotoxin type B | protein | 217 | 18% helix, 40% strand | P01552 |
| E | Peptide from collagen II | protein | 12 | 0% helix, 17% strand | P02458 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, B
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 | 227 | 0.49 | 0.75 | 27 | empty |
| 2 | 184 | 0.47 | 0.75 | 29 | empty |
| 3 | 77 | 0.30 | 0.73 | 15 | empty |
| 4 | 51 | 0.24 | 0.72 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2532 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 722 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 604 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 534 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2SEB · X-ray crystal structure of HLA-DR4 complexed with a peptide from human collagen II · 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 D 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
- P02458 · AlphaFold monomer V2.0 prediction for collagen alpha-1(II) chain (P02458) · a predicted model of the same protein · chain E against A, TM-score 0.40
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
- Every structure of UniProt P02458
- Elsewhere: RCSB PDB 2SEB · PDBe 2SEB · UniProt P01903 · UniProt P13760 · UniProt P01552 · UniProt P02458
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