MolNFT v1 · #173134 · protein
Clip peptide bound to chicken MHC class II molecule (bl-2) from B2 haplotype with a decamer mode of binding
7APZ · MHC class II alpha chain: “Clip peptide bound to chicken MHC class II molecule (bl-2) from B2 haplotype with a decamer mode of binding”. X-ray diffraction, 4 ligands (ACE, NAG, ZN), 3 pockets (best druggability 0.60). MolNFT v1…
- PDB
- 7APZ
- Type
- protein
- Length
- 390 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II alpha chain; MHC class II beta chain 2
- UniProt
- Q4U5Z6, B5BSA0
- Ligands
- ACE, NAG, ZN, NI
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II alpha chain | protein | 184 | 15% helix, 48% strand | Q4U5Z6 |
| B | MHC class II beta chain 2 | protein | 206 | 17% helix, 41% strand | B5BSA0 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 10 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, A
- ZN · Zinc ion · metal · 10 copies · chains A, B
- NI · Nickel (II) ion · metal · chains B
- IMD · Imidazole · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 247 | 0.60 | 0.80 | 46 | IMD, ACE |
| 2 | 167 | 0.43 | 0.74 | 25 | empty |
| 3 | 97 | 0.33 | 0.73 | 22 | ZN |
Interfaces
1 interface between chains.
- A–B · 3164 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7APZ · CLIP peptide bound to chicken MHC class II molecule (BL-2) from B2 haplotype with a… · 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 B5BSA0
- Elsewhere: RCSB PDB 7APZ · PDBe 7APZ · UniProt Q4U5Z6 · UniProt B5BSA0
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