MolNFT v1 · #63934 · protein
Crystal structure of the class I MHC molecule H-2KWM7 with a single self peptide iqqsierl
3FOM: “Crystal structure of the class I MHC molecule H-2KWM7 with a single self peptide iqqsierl”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.65). MolNFT v1 #63934 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3FOM
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC; Beta-2-microglobulin; 8 residue synthetic peptide
- UniProt
- P01887
- Ligands
- CL
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC | protein | 274 | 27% helix, 41% strand | — |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P01887 |
| P | 8 residue synthetic peptide | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.65 | 0.76 | 57 | empty |
| 2 | 144 | 0.48 | 0.78 | 28 | empty |
| 3 | 66 | 0.34 | 0.76 | 16 | empty |
| 4 | 55 | 0.28 | 0.74 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1269 Ų buried · 23 hydrogen bonds · protein-protein
- A–P · 918 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3FOM · Crystal structure of the Class I MHC Molecule H-2Kwm7 with a Single Self Peptide IQQSIERL · the same entry in another collection · chain A against A, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B 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 P01887
- Elsewhere: RCSB PDB 3FOM · PDBe 3FOM · UniProt P01887
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