Research workbench
HLA-DRB1 in complex with citrullinated LL37 peptide
Analyse HLA-DRB1 in complex with citrullinated LL37 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BIX
- Type
- protein
- Length
- 379 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 dr-beta (HLA-dr B)…
- UniProt
- P01903, Q29890
- Ligands
- CIR, NAG
- Pockets
- 4 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 14% helix, 46% strand | P01903 |
| B | HLA class II dr-beta (HLA-dr B) | protein | 189 | 19% helix, 45% strand | Q29890 |
| C | LL37_CIT91 | protein | 12 | 0% helix, 8% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · 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 | 162 | 0.44 | 0.74 | 22 | empty |
| 2 | 94 | 0.41 | 0.78 | 17 | empty |
| 3 | 57 | 0.40 | 0.81 | 12 | CIR |
| 4 | 58 | 0.26 | 0.72 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2457 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 598 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 547 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6BIX · HLA-DRB1 in complex with citrullinated LL37 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
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 Q29890
- Elsewhere: RCSB PDB 6BIX · PDBe 6BIX · UniProt P01903 · UniProt Q29890
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