MolNFT v1 · #172238 · protein
Clip peptide bound to chicken MHC class II molecule (bl-2) from B19 haplotype
6ZWA · MHC class II alpha chain: “Clip peptide bound to chicken MHC class II molecule (bl-2) from B19 haplotype”. X-ray diffraction, 3 pockets (best druggability 0.62). MolNFT v1 #172238 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ZWA
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II alpha chain; Invariant chain isoform P41,MHC class II beta chain 2
- UniProt
- Q4U5Z6, Q6J613, A5HUL4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II alpha chain | protein | 183 | 14% helix, 49% strand | Q4U5Z6 |
| B | Invariant chain isoform P41,MHC class II beta chain 2 | protein | 193 | 17% helix, 44% strand | Q6J613, A5HUL4 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.62 | 0.82 | 34 | empty |
| 2 | 142 | 0.46 | 0.77 | 22 | empty |
| 3 | 119 | 0.38 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3048 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6ZWA · CLIP peptide bound to chicken MHC class II molecule (BL-2) from B19 haplotype · 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 Q4U5Z6
- Every structure of UniProt Q6J613
- Every structure of UniProt A5HUL4
- Elsewhere: RCSB PDB 6ZWA · PDBe 6ZWA · UniProt Q4U5Z6 · UniProt Q6J613 · UniProt A5HUL4
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