MolNFT v1 · #83332 · protein
Crystal structure of HLA-DP5 in complex with cry J 1-derived peptide (residues 214-222)
3WEX · MHC class II antigen: “Crystal structure of HLA-DP5 in complex with cry J 1-derived peptide (residues 214-222)”. X-ray diffraction, 1 ligand (NAG), 17 pockets (best druggability 0.69). MolNFT v1 #83332 on GenesisL1: 3D structure…
- PDB
- 3WEX
- Type
- protein
- Length
- 1,504 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II antigen
- UniProt
- I2G9G1, I2FL84
- Ligands
- NAG
- Pockets
- 17 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | MHC class II antigen | protein | 181 | 14% helix, 45% strand | I2G9G1 |
| B, D, F, H | MHC class II antigen | protein | 195 | 18% helix, 44% strand | I2FL84 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.69 | 0.80 | 56 | empty |
| 2 | 479 | 0.69 | 0.80 | 63 | empty |
| 3 | 392 | 0.68 | 0.81 | 47 | empty |
| 4 | 290 | 0.63 | 0.80 | 37 | empty |
| 5 | 254 | 0.59 | 0.80 | 35 | empty |
Interfaces
14 interfaces between chains.
- G–H · 3111 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 3081 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 3064 Ų buried · 59 hydrogen bonds · protein-protein
- E–F · 3035 Ų buried · 59 hydrogen bonds · protein-protein
- D–E · 468 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3WEX · Crystal structure of HLA-DP5 in complex with Cry j 1-derived peptide (residues 214-222) · the same entry in another collection · chain C against C, 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 I2G9G1
- Every structure of UniProt I2FL84
- Elsewhere: RCSB PDB 3WEX · PDBe 3WEX · UniProt I2G9G1 · UniProt I2FL84
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