Research workbench
Conformational restraints and flexibility of 14-meric peptides in complex with HLA-B*3501
Analyse Conformational restraints and flexibility of 14-meric peptides in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XH3
- Type
- protein
- Length
- 389 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-35 alpha chain; Beta-2-microglobulin; Aa 4-17…
- UniProt
- P30685, P61769
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-35 alpha chain | protein | 276 | 27% helix, 39% strand | P30685 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Aa 4-17 (lpavvglspgeqey) of alternative reading frame of M- csf | protein | 14 | 21% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.69 | 0.77 | 54 | empty |
| 2 | 73 | 0.68 | 0.94 | 19 | empty |
| 3 | 105 | 0.43 | 0.78 | 20 | empty |
| 4 | 95 | 0.42 | 0.78 | 24 | empty |
| 5 | 58 | 0.35 | 0.78 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1345 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 942 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1XH3 · Conformational Restraints and Flexibility of 14-Meric Peptides in Complex with HLA-B*3501 · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P30685
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 1XH3 · PDBe 1XH3 · UniProt P30685 · UniProt P61769
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