Research workbench
MHC class I in complex with modified sendai virus nucleoprotein peptide FAPGN(3,5-DIIODOTYROSINE)PAL
Analyse MHC class I in complex with modified sendai virus nucleoprotein peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PGC
- Type
- protein
- Length
- 785 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin; Sendai…
- UniProt
- P01901, P01887
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 278 | 27% helix, 38% strand | P01901 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F | Sendai virus nucleoprotein | protein | 9 | 0% helix, 0% strand | — |
| H | Unknown helical fragment | protein | 13 | 85% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B, H, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.69 | 0.75 | 81 | GOL |
| 2 | 712 | 0.66 | 0.75 | 60 | empty |
| 3 | 176 | 0.56 | 0.80 | 32 | empty |
| 4 | 150 | 0.52 | 0.79 | 27 | empty |
| 5 | 166 | 0.44 | 0.75 | 26 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1221 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1211 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 810 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 802 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 637 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 4PGC · MHC Class I in complex with modified Sendai virus nucleoprotein peptide… · the same entry in another collection · chain C against C, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P01901
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 4PGC · PDBe 4PGC · UniProt P01901 · UniProt P01887
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