Research workbench
Crystal structure of DQA1*01:02/DQB1*06:02 in complex with a hypocretin peptide
Analyse Crystal structure of DQA1*01:02/DQB1*06:02 in complex with a hypocretin peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DIG
- Type
- protein
- Length
- 375 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II HLA-dq-alpha chain; HLA class II histocompatibility antigen, dq beta 1…
- UniProt
- Q30066, Q5SU54
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II HLA-dq-alpha chain | protein | 182 | 14% helix, 44% strand | Q30066 |
| B | HLA class II histocompatibility antigen, dq beta 1 chain | protein | 180 | 21% helix, 45% strand | Q5SU54 |
| C | 13-mer peptide: ala-gly-asn-his-ala-ala-gly-ile-leu-thr- leu-gly-lys | protein | 13 | 0% helix, 15% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.55 | 0.75 | 44 | TRS |
| 2 | 74 | 0.32 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2671 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 653 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 602 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6DIG · Crystal structure of DQA1*01:02/DQB1*06:02 in complex with a hypocretin peptide · the same entry in another collection · chain A against A, 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 Q30066
- Every structure of UniProt Q5SU54
- Elsewhere: RCSB PDB 6DIG · PDBe 6DIG · UniProt Q30066 · UniProt Q5SU54
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.