MolNFT v1 · #40371 · protein
Crystal structure of the MHC class II molecule HLA-DR1 in complex with the fluorogenic peptide, acpkxvkqntlklat (X=3-[5-(dimethylamino)-1,3- dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) and the superantigen, SEC3 variant 3B2
2IPK · HLA class II histocompatibility antigen, dr alpha chain: “Crystal structure of the MHC class II molecule HLA-DR1 in complex with the fluorogenic peptide…”. X-ray diffraction, 1 ligand (ACE), 6 pockets (best druggability 0.50).…
- PDB
- 2IPK
- Type
- protein
- Length
- 614 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
- UniProt
- P01903, P04229, P0A0L3
- Ligands
- ACE
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 13% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 190 | 19% helix, 45% strand | P04229 |
| C | Ha related fluorogenic peptide, acpkxvkqntlklat (X=3-[5- (dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) | protein | 13 | 0% helix, 8% strand | — |
| D | Enterotoxin type C-3 | protein | 232 | 19% helix, 33% strand | P0A0L3 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.50 | 0.75 | 26 | empty |
| 2 | 204 | 0.50 | 0.76 | 26 | empty |
| 3 | 72 | 0.43 | 0.80 | 16 | empty |
| 4 | 155 | 0.42 | 0.74 | 32 | empty |
| 5 | 85 | 0.35 | 0.75 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2575 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 774 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 757 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 732 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 2IPK · Crystal Structure of the MHC Class II Molecule HLA-DR1 in Complex with the Fluorogenic… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A0L3 · AlphaFold monomer V2.0 prediction for enterotoxin type C-3 (P0A0L3) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr 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 P01903
- Every structure of UniProt P04229
- Every structure of UniProt P0A0L3
- Elsewhere: RCSB PDB 2IPK · PDBe 2IPK · UniProt P01903 · UniProt P04229 · UniProt P0A0L3
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