Research workbench
Crystal structure of HLA-DRB1*04:01 in complex with modified alpha- enolase peptide 26-40 with citrulline at the position 32
Analyse Crystal structure of HLA-DRB1*04:01 in complex with modified alpha- enolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JLZ
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- 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, K7EM90
- Ligands
- CIR
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 14% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 193 | 18% helix, 45% strand | P13760 |
| C | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 14% helix, 46% strand | P01903 |
| D | HLA class II histocompatibility antigen, DRB1-4 beta chain | protein | 190 | 18% helix, 45% strand | P13760 |
| E, F | Alpha-enolase | protein | 13 | 0% helix, 15% strand | K7EM90 |
Ligands and binding sites
- CIR · Citrulline · ligand · 2 copies · chains A, B, E, C, D, F
- MLA · Malonic acid · additive · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.78 | 0.80 | 106 | empty |
| 2 | 458 | 0.70 | 0.80 | 53 | empty |
| 3 | 100 | 0.49 | 0.81 | 21 | empty |
| 4 | 64 | 0.40 | 0.80 | 21 | empty |
| 5 | 98 | 0.39 | 0.76 | 16 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2586 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2559 Ų buried · 42 hydrogen bonds · protein-protein
- A–E · 651 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 639 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 531 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 covalent (disulfide, covalent ligand).
Compared structures
- 5JLZ · Crystal structure of HLA-DRB1*04:01 in complex with modified alpha-enolase peptide 26-40… · the same entry in another collection · chain F against F, 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
- Every structure of UniProt K7EM90
- Elsewhere: RCSB PDB 5JLZ · PDBe 5JLZ · UniProt P01903 · UniProt P13760 · UniProt K7EM90
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