Research workbench
Crystal structure of H2DB-NPM6T
Analyse Crystal structure of H2DB-NPM6T in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HUW
- Type
- protein
- Length
- 1,544 residues
- Chains
- 12
- 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; NPM6T…
- UniProt
- P01899, P01887
- Ligands
- SO4
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 277 | 29% helix, 38% strand | P01899 |
| B, D, F, H | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P01887 |
| I, J, K, L | NPM6T variant peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.74 | 0.81 | 62 | SO4 |
| 2 | 725 | 0.74 | 0.79 | 78 | SO4 |
| 3 | 569 | 0.72 | 0.80 | 82 | empty |
| 4 | 848 | 0.71 | 0.77 | 75 | empty |
| 5 | 633 | 0.68 | 0.77 | 51 | empty |
Interfaces
20 interfaces between chains.
- E–F · 1316 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1296 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1280 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1272 Ų buried · 20 hydrogen bonds · protein-protein
- C–J · 876 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4HUW · Crystal Structure of H2Db-NPM6T · the same entry in another collection · chain L against L, TM-score 1.00
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 4HUW · PDBe 4HUW · UniProt P01899 · UniProt P01887
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