MolNFT v1 · #171579 · protein
Human class I major histocompatibility complex, A02 allele, presenting llgwvfaqv
6Z9W · MHC class I antigen: “Human class I major histocompatibility complex, A02 allele, presenting llgwvfaqv”. X-ray diffraction, 13 pockets (best druggability 0.69). MolNFT v1 #171579 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6Z9W
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Leu-leu-gly-TRP-val-phe-ala-gln-val
- UniProt
- U5YJM1, P61769
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class I antigen | protein | 275 | 27% helix, 39% strand | U5YJM1 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Leu-leu-gly-TRP-val-phe-ala-gln-val | protein | 9 | 0% helix, 0% strand | — |
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.69 | 0.78 | 57 | empty |
| 2 | 584 | 0.69 | 0.78 | 47 | empty |
| 3 | 371 | 0.61 | 0.77 | 55 | empty |
| 4 | 197 | 0.50 | 0.76 | 27 | empty |
| 5 | 124 | 0.48 | 0.79 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1437 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1412 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 870 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 857 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 232 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6Z9W · Human Class I Major Histocompatibility Complex, A02 allele, presenting LLGWVFAQV · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E 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 U5YJM1
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6Z9W · PDBe 6Z9W · UniProt U5YJM1 · UniProt P61769
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