Research workbench
Crystal structure of H-2DB with the GAP501 peptide (sql)
Analyse Crystal structure of H-2DB with the GAP501 peptide (sql) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WLG
- Type
- protein
- Length
- 1,612 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin; GAP50…
- UniProt
- P01899, P01887, A0A0Y9W4B5, A0A075B616, K7N5M3, P04213, K7N5M4
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 8 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 278 | 24% helix, 37% strand | P01899 |
| B, G | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
| C, H | GAP50 peptide | protein | 9 | 0% helix, 0% strand | A0A0Y9W4B5 |
| D | T cell receptor alpha variable 8D-2,HUMAN nkt TCR alpha chain | protein | 182 | 5% helix, 49% strand | A0A075B616, K7N5M3 |
| E | T-cell receptor beta chain V region C5,HUMAN nkt TCR beta chain | protein | 243 | 7% helix, 48% strand | P04213, K7N5M4 |
| F | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 277 | 25% helix, 38% strand | P01899 |
| I | T cell receptor alpha variable 8D-2,HUMAN nkt TCR alpha chain | protein | 177 | 2% helix, 49% strand | A0A075B616, K7N5M3 |
| J | T-cell receptor beta chain V region C5,HUMAN nkt TCR beta chain | protein | 241 | 7% helix, 46% strand | P04213, K7N5M4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.77 | 0.80 | 84 | empty |
| 2 | 723 | 0.74 | 0.80 | 93 | empty |
| 3 | 1101 | 0.74 | 0.77 | 77 | empty |
| 4 | 592 | 0.66 | 0.76 | 54 | NA |
| 5 | 540 | 0.64 | 0.76 | 52 | NA, CL |
Interfaces
21 interfaces between chains.
- D–E · 2157 Ų buried · 22 hydrogen bonds · protein-protein
- I–J · 2086 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 1203 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1156 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 958 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
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 P01899
- Every structure of UniProt P01887
- Every structure of UniProt A0A0Y9W4B5
- Every structure of UniProt A0A075B616
- Every structure of UniProt K7N5M3
- Every structure of UniProt P04213
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 5WLG · PDBe 5WLG · UniProt P01899 · UniProt P01887 · UniProt A0A0Y9W4B5 · UniProt A0A075B616 · UniProt K7N5M3 · UniProt P04213 · UniProt K7N5M4
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