MolNFT v1 · #60536 · protein
Crystal structure of the MHC class II molecule I-AG7 in complex with the peptide GAD221-235
3CUP · H-2 class II histocompatibility antigen, a-D alpha chain: “Crystal structure of the MHC class II molecule I-AG7 in complex with the peptide GAD221-235”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.53). MolNFT…
- PDB
- 3CUP
- Type
- protein
- Length
- 358 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class II histocompatibility antigen, a-D alpha chain; MHC class II H2-ia-beta chain…
- UniProt
- P04228, Q6LDA5, Q31135
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class II histocompatibility antigen, a-D alpha chain | protein | 182 | 14% helix, 47% strand | P04228 |
| B | MHC class II H2-ia-beta chain linked to GAD221-235 peptide | protein | 176 | 20% helix, 40% strand | Q6LDA5, Q31135 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, 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 | 280 | 0.53 | 0.75 | 40 | EPE |
| 2 | 89 | 0.37 | 0.76 | 19 | empty |
| 3 | 92 | 0.32 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3027 Ų buried · 60 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3CUP · Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- P04228 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P04228
- Every structure of UniProt Q6LDA5
- Every structure of UniProt Q31135
- Elsewhere: RCSB PDB 3CUP · PDBe 3CUP · UniProt P04228 · UniProt Q6LDA5 · UniProt Q31135
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