MolNFT v1 · #92323 · protein
Structure of the chicken MHC class I molecule BF2*0401 complexed to pepitde P8D
4G42 · MHC class I alpha chain 2: “Structure of the chicken MHC class I molecule BF2*0401 complexed to pepitde P8D”. X-ray diffraction, 6 pockets (best druggability 0.69). MolNFT v1 #92323 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4G42
- Type
- protein
- Length
- 753 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I alpha chain 2; Beta-2 microglobulin; 8-meric peptide P8D
- UniProt
- O46790, P21611
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I alpha chain 2 | protein | 271 | 28% helix, 38% strand | O46790 |
| B, E | Beta-2 microglobulin | protein | 97 | 0% helix, 52% strand | P21611 |
| C, F | 8-meric peptide P8D | protein | 8 | 0% helix, 0% strand | — |
| D | MHC class I alpha chain 2 | protein | 272 | 29% helix, 40% strand | O46790 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.69 | 0.79 | 52 | empty |
| 2 | 481 | 0.68 | 0.79 | 43 | empty |
| 3 | 280 | 0.55 | 0.76 | 30 | empty |
| 4 | 161 | 0.54 | 0.80 | 22 | empty |
| 5 | 119 | 0.47 | 0.79 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1561 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1432 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 880 Ų buried · 29 hydrogen bonds · protein-protein
- D–F · 864 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 275 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4G42 · Structure of the Chicken MHC Class I Molecule BF2*0401 complexed to pepitde P8D · the same entry in another collection · chain F against F, TM-score 1.00
- P21611 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P21611) · a predicted model of the same protein · chain B 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 O46790
- Every structure of UniProt P21611
- Elsewhere: RCSB PDB 4G42 · PDBe 4G42 · UniProt O46790 · UniProt P21611
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