Research workbench
Crystallographic structure of a rheumatoid arthritis MHC susceptibility allele, HLA-DR1 (DRB1*0101), complexed with the immunodominant determinant of human type II collagen
Analyse Crystallographic structure of a rheumatoid arthritis MHC susceptibility allele… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FSE
- Type
- protein
- Length
- 755 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class II histocompatibility antigen, E-K alpha chain; HLA class II histocompatibility…
- UniProt
- P01903, P04229, P02458
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class II histocompatibility antigen, E-K alpha chain | protein | 178 | 14% helix, 45% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 186 | 18% helix, 47% strand | P04229 |
| C | H-2 class II histocompatibility antigen, E-K alpha chain | protein | 177 | 14% helix, 46% strand | P01903 |
| D | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 186 | 20% helix, 43% strand | P04229 |
| E, F | Collagen alpha-1(II) | protein | 14 | 0% helix, 0% strand | P02458 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 729 | 0.82 | 0.85 | 70 | empty |
| 2 | 381 | 0.78 | 0.87 | 52 | empty |
| 3 | 220 | 0.62 | 0.81 | 24 | empty |
| 4 | 104 | 0.41 | 0.77 | 17 | empty |
| 5 | 141 | 0.40 | 0.74 | 27 | empty |
Interfaces
9 interfaces between chains.
- C–D · 2577 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2481 Ų buried · 35 hydrogen bonds · protein-protein
- B–E · 614 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 613 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 597 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2FSE · Crystallographic structure of a rheumatoid arthritis MHC susceptibility allele, HLA-DR1… · 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 C against A, TM-score 0.96
- 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 0.36
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 P04229
- Every structure of UniProt P02458
- Elsewhere: RCSB PDB 2FSE · PDBe 2FSE · UniProt P01903 · UniProt P04229 · UniProt P02458
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