MolNFT v1 · #92324 · protein
Structure of the chicken MHC class I molecule BF2*0401 complexed to P5E
4G43 · MHC class I alpha chain 2: “Structure of the chicken MHC class I molecule BF2*0401 complexed to P5E”. X-ray diffraction, 7 pockets (best druggability 0.66). MolNFT v1 #92324 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4G43
- Type
- protein
- Length
- 752 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 P5E
- UniProt
- O46790, P21611
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I alpha chain 2 | protein | 272 | 28% helix, 40% strand | O46790 |
| B, E | Beta-2 microglobulin | protein | 97 | 0% helix, 48% strand | P21611 |
| C, F | 8-meric peptide P5E | protein | 8 | 0% helix, 0% strand | — |
| D | MHC class I alpha chain 2 | protein | 270 | 27% helix, 41% strand | O46790 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.66 | 0.79 | 56 | empty |
| 2 | 461 | 0.66 | 0.78 | 48 | empty |
| 3 | 153 | 0.52 | 0.79 | 21 | empty |
| 4 | 219 | 0.51 | 0.76 | 26 | empty |
| 5 | 130 | 0.49 | 0.79 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1553 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1484 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 894 Ų buried · 32 hydrogen bonds · protein-protein
- D–F · 888 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 282 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4G43 · Structure of the chicken MHC class I molecule BF2*0401 complexed to P5E · 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 0.97
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 4G43 · PDBe 4G43 · UniProt O46790 · UniProt P21611
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