MolNFT v1 · #9898 · protein
Histocompatibility antigen I-ak
1IAK · MHC class II I-ak: “Histocompatibility antigen I-ak”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.52). MolNFT v1 #9898 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1IAK
- Type
- protein
- Length
- 380 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II I-ak
- UniProt
- P01910, P06343, P24364
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II I-ak | protein | 182 | 15% helix, 45% strand | P01910 |
| B | MHC class II I-ak | protein | 185 | 21% helix, 46% strand | P06343 |
| P | MHC class II I-ak | protein | 13 | 0% helix, 8% strand | P24364 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · 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 | 0.52 | 0.74 | 35 | empty |
| 2 | 114 | 0.41 | 0.76 | 23 | empty |
| 3 | 120 | 0.36 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2578 Ų buried · 51 hydrogen bonds · protein-protein
- B–P · 763 Ų buried · 9 hydrogen bonds · protein-protein
- A–P · 699 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1IAK · Histocompatibility antigen I-ak · the same entry in another collection · chain A against A, TM-score 1.00
- P01910 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-K alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P06343 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-K beta… · a predicted model of the same protein · chain B against A, TM-score 0.96
- P24364 · AlphaFold monomer V2.0 prediction for lysozyme C (P24364) · a predicted model of the same protein · chain P against A, TM-score 0.32
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 P01910
- Every structure of UniProt P06343
- Every structure of UniProt P24364
- Elsewhere: RCSB PDB 1IAK · PDBe 1IAK · UniProt P01910 · UniProt P06343 · UniProt P24364
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