MolNFT v1 · #63935 · protein
Crystal structure of the class I MHC molecule H-2KWM7 with a single self peptide vndifeai
3FON: “Crystal structure of the class I MHC molecule H-2KWM7 with a single self peptide vndifeai”. X-ray diffraction, 8 pockets (best druggability 0.66). MolNFT v1 #63935 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3FON
- Type
- protein
- Length
- 764 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC; Beta-2-microglobulin; Peptide
- UniProt
- P01887
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | MHC | protein | 274 | 28% helix, 41% strand | — |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P01887 |
| P, E | Peptide | protein | 8 | 0% helix, 0% strand | — |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 663 | 0.66 | 0.75 | 60 | empty |
| 2 | 601 | 0.64 | 0.75 | 57 | empty |
| 3 | 151 | 0.44 | 0.75 | 27 | empty |
| 4 | 130 | 0.43 | 0.76 | 26 | empty |
| 5 | 127 | 0.39 | 0.74 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1357 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1350 Ų buried · 20 hydrogen bonds · protein-protein
- A–P · 836 Ų buried · 28 hydrogen bonds · protein-protein
- C–E · 834 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 196 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3FON · Crystal structure of the Class I MHC Molecule H-2Kwm7 with a Single Self Peptide VNDIFEAI · the same entry in another collection · chain E against E, 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 0.98
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 3FON · PDBe 3FON · UniProt P01887
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