Research workbench
HLA-DRB1 in complex with citrullinated fibrinogen peptide
Analyse HLA-DRB1 in complex with citrullinated fibrinogen peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BIJ
- Type
- protein
- Length
- 377 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
- Ligands
- CIR, NAG
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 177 | 14% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 189 | 17% helix, 45% strand | P13760 |
| C | Citrullinated fibrinogen 72,74CIT69-81 | protein | 11 | 0% helix, 9% strand | — |
Ligands and binding sites
- CIR · Citrulline · ligand · 2 copies · 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
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 | 132 | 0.41 | 0.75 | 26 | empty |
| 2 | 63 | 0.37 | 0.79 | 19 | CIR |
| 3 | 83 | 0.33 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2464 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 533 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 512 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 3 disulfide, 2 glycan (covalent ligand, disulfide, N-glycosylation).
Compared structures
- 6BIJ · HLA-DRB1 in complex with citrullinated fibrinogen 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 P13760
- Elsewhere: RCSB PDB 6BIJ · PDBe 6BIJ · UniProt P01903 · UniProt P13760
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