MolNFT v1 · #171578 · protein
Human class I major histocompatibility complex, A02 allele, presenting iigwmwipv
6Z9V · MHC class I antigen: “Human class I major histocompatibility complex, A02 allele, presenting iigwmwipv”. X-ray diffraction, 4 ligands (P4G, NA, CA), 9 pockets (best druggability 0.75). MolNFT v1 #171578 on GenesisL1: 3D structure…
- PDB
- 6Z9V
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Ile-ile-gly-TRP-met-TRP-ile-pro-val
- UniProt
- A0A5B8RNS7, P61769
- Ligands
- P4G, NA, CA, SO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | MHC class I antigen | protein | 276 | 26% helix, 40% strand | A0A5B8RNS7 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Ile-ile-gly-TRP-met-TRP-ile-pro-val | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 2 copies · chains A, C, D, F
- NA · Sodium ion · metal · chains B
- CA · Calcium ion · metal · chains E
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, C, B, D, E
- GOL · Glycerol · additive · 6 copies · chains A, B, D, F, E
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.75 | 0.78 | 90 | EDO, GOL |
| 2 | 907 | 0.74 | 0.78 | 87 | SO4 |
| 3 | 81 | 0.48 | 0.82 | 20 | EDO, P4G |
| 4 | 140 | 0.47 | 0.78 | 26 | empty |
| 5 | 76 | 0.45 | 0.81 | 19 | EDO |
Interfaces
7 interfaces between chains.
- A–B · 1405 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1374 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 907 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 875 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 462 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6Z9V · Human Class I Major Histocompatibility Complex, A02 allele, presenting IIGWMWIPV · 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 A0A5B8RNS7
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6Z9V · PDBe 6Z9V · UniProt A0A5B8RNS7 · UniProt P61769
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