Research workbench
Crystal structure of H2-dd with disulfide-linked 6MER peptide
Analyse Crystal structure of H2-dd with disulfide-linked 6MER peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WET
- Type
- protein
- Length
- 380 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-D alpha chain; Beta-2-microglobulin; Surface…
- UniProt
- P01900, P01887, P03377
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-D alpha chain | protein | 275 | 28% helix, 39% strand | P01900 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 55% strand | P01887 |
| P | Surface protein GP120 | protein | 6 | 0% helix, 0% strand | P03377 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.63 | 0.75 | 53 | empty |
| 2 | 89 | 0.62 | 0.89 | 19 | empty |
| 3 | 64 | 0.47 | 0.84 | 17 | empty |
| 4 | 102 | 0.42 | 0.77 | 21 | empty |
| 5 | 54 | 0.36 | 0.79 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1217 Ų buried · 21 hydrogen bonds · protein-protein
- A–P · 534 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5WET · Crystal Structure of H2-Dd with disulfide-linked 6mer peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P01900 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, D-D 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 P01900
- Every structure of UniProt P01887
- Every structure of UniProt P03377
- Elsewhere: RCSB PDB 5WET · PDBe 5WET · UniProt P01900 · UniProt P01887 · UniProt P03377
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