Research workbench
Class I MHC (HLA-A*02) presenting alpha fetoprotein peptide (afp)
Analyse Class I MHC (HLA-A*02) presenting alpha fetoprotein peptide (afp) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RE8
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen, a-2 alpha chain; Beta-2-microglobulin…
- UniProt
- A0A5B8RNS7, P61769
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class I antigen, a-2 alpha chain | protein | 275 | 27% helix, 40% strand | A0A5B8RNS7 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Phe-met-asn-lys-phe-ile-tyr-glu-ile | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B, D, E
- PGE · Triethylene glycol · additive · 6 copies · chains A, B, C, D, F, E
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.76 | 0.79 | 109 | PEG, PGE |
| 2 | 456 | 0.69 | 0.80 | 42 | PEG |
| 3 | 104 | 0.44 | 0.78 | 17 | 1PE |
| 4 | 94 | 0.42 | 0.78 | 19 | 1PE |
| 5 | 77 | 0.38 | 0.78 | 17 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1435 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1433 Ų buried · 26 hydrogen bonds · protein-protein
- F–D · 955 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 942 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 467 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 A0A5B8RNS7
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7RE8 · PDBe 7RE8 · UniProt A0A5B8RNS7 · UniProt P61769
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