Research workbench
Crystal structure of H2DB-H155A-NPM6I
Analyse Crystal structure of H2DB-H155A-NPM6I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HV8
- Type
- protein
- Length
- 771 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; NPM6I…
- UniProt
- P01899, P01887
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 276 | 27% helix, 39% strand | P01899 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P01887 |
| C | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 278 | 27% helix, 38% strand | P01899 |
| D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| E, F | NPM6I variant peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.76 | 0.78 | 113 | empty |
| 2 | 83 | 0.47 | 0.82 | 18 | empty |
| 3 | 141 | 0.46 | 0.77 | 36 | empty |
| 4 | 84 | 0.45 | 0.80 | 17 | empty |
| 5 | 110 | 0.40 | 0.75 | 22 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1326 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1183 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 856 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 843 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 803 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 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
- Elsewhere: RCSB PDB 4HV8 · PDBe 4HV8 · UniProt P01899 · UniProt P01887
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