Research workbench
H-2DB complex with human GP100
Analyse H-2DB complex with human GP100 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CC5
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- 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; Nonameric…
- UniProt
- P01899, P01887, P40967
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 276 | 27% helix, 39% strand | P01899 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F | Nonameric peptide from melanocyte protein pmel 17 | protein | 9 | 0% helix, 0% strand | P40967 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, D
- GOL · Glycerol · additive · 6 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.69 | 0.76 | 66 | GOL |
| 2 | 675 | 0.66 | 0.75 | 61 | GOL |
| 3 | 161 | 0.45 | 0.75 | 31 | empty |
| 4 | 93 | 0.44 | 0.79 | 15 | empty |
| 5 | 90 | 0.43 | 0.79 | 16 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1222 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1217 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 1016 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1015 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 654 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3CC5 · H-2Db complex with human gp100 · the same entry in another collection · chain F against F, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain E against A, TM-score 0.98
- P40967 · AlphaFold monomer V2.0 prediction for melanocyte protein pmel (P40967) · a predicted model of the same protein · chain C against A, TM-score 0.50
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 P40967
- Elsewhere: RCSB PDB 3CC5 · PDBe 3CC5 · UniProt P01899 · UniProt P01887 · UniProt P40967
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