MolNFT v1 · #94373 · protein
Crystal structure of H2DB-NPM6W
4HUV · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structure of H2DB-NPM6W”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.77). MolNFT v1 #94373 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4HUV
- Type
- protein
- Length
- 765 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; NPM6W…
- UniProt
- P01899, P01887
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 275 | 25% helix, 37% strand | P01899 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P01887 |
| C, F | NPM6W variant peptide | protein | 9 | 0% helix, 0% strand | — |
| E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.77 | 0.79 | 101 | SO4 |
| 2 | 704 | 0.68 | 0.76 | 63 | empty |
| 3 | 651 | 0.66 | 0.75 | 55 | empty |
| 4 | 96 | 0.44 | 0.79 | 17 | empty |
| 5 | 82 | 0.41 | 0.78 | 14 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1177 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1163 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 936 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 934 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 320 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 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 4HUV · PDBe 4HUV · UniProt P01899 · UniProt P01887
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