MolNFT v1 · #182699 · protein
DR3 in complex with aspergillus nidulans NAD-dependent histone deacetylase HST4 peptide
7N19 · HLA class II histocompatibility antigen, dr alpha chain: “DR3 in complex with aspergillus nidulans NAD-dependent histone deacetylase HST4 peptide”. X-ray diffraction, 1 ligand (NAG), 19 pockets (best druggability 0.66). MolNFT v1…
- PDB
- 7N19
- Type
- protein
- Length
- 1,516 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
- UniProt
- P01903, Q5Y7D1
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 14% helix, 47% strand | P01903 |
| B, E, H, K | HLA class II histocompatibility antigen dr beta chain | protein | 187 | 17% helix, 45% strand | Q5Y7D1 |
| C, F, I, L | HST4 peptide | protein | 13 | 0% helix, 15% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains G, A, D, J, B, H, K
- EDO · 1,2-ethanediol · additive · 30 copies · chains A, B, J, C, D, H, E, G, I, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.66 | 0.79 | 42 | empty |
| 2 | 392 | 0.64 | 0.79 | 40 | empty |
| 3 | 189 | 0.53 | 0.78 | 28 | empty |
| 4 | 128 | 0.52 | 0.81 | 27 | EDO |
| 5 | 126 | 0.52 | 0.81 | 27 | EDO |
Interfaces
21 interfaces between chains.
- A–B · 2503 Ų buried · 41 hydrogen bonds · protein-protein
- D–E · 2486 Ų buried · 41 hydrogen bonds · protein-protein
- J–K · 2453 Ų buried · 40 hydrogen bonds · protein-protein
- G–H · 2424 Ų buried · 36 hydrogen bonds · protein-protein
- K–L · 714 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7N19 · DR3 in complex with Aspergillus nidulans NAD-dependent histone deacetylase hst4 peptide · 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 P01903
- Every structure of UniProt Q5Y7D1
- Elsewhere: RCSB PDB 7N19 · PDBe 7N19 · UniProt P01903 · UniProt Q5Y7D1
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