Research workbench
HLA-DR1 mutant BN82A with covalently linked CLIP106-120(M107W)
Analyse HLA-DR1 mutant BN82A with covalently linked CLIP106-120(M107W) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X5X
- Type
- protein
- Length
- 752 residues
- Chains
- 4
- 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, P04229
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 13% helix, 47% strand | P01903 |
| B, D | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 198 | 15% helix, 41% strand | P04229 |
| C | HLA class II histocompatibility antigen, dr alpha chain | protein | 177 | 14% helix, 47% strand | P01903 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.64 | 0.75 | 48 | empty |
| 2 | 459 | 0.59 | 0.74 | 51 | empty |
| 3 | 91 | 0.34 | 0.73 | 17 | empty |
| 4 | 73 | 0.31 | 0.74 | 17 | empty |
| 5 | 65 | 0.29 | 0.74 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3084 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3017 Ų buried · 55 hydrogen bonds · protein-protein
- B–D · 153 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 148 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4X5X · HLA-DR1 mutant bN82A with covalently linked CLIP106-120(M107W) · 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 C against A, TM-score 0.97
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
- Elsewhere: RCSB PDB 4X5X · PDBe 4X5X · UniProt P01903 · UniProt P04229
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