MolNFT v1 · #152292 · protein
Defining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01
6ID4 · MHC class I antigen: “Defining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01”. X-ray diffraction, 18 pockets (best druggability 0.78). MolNFT v1 #152292 on GenesisL1: 3D structure…
- PDB
- 6ID4
- Type
- protein
- Length
- 1,628 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Heavy chain; Light chain; Peptide
- UniProt
- F6IQY1, P61769
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 274 | 27% helix, 40% strand | F6IQY1 |
| B, F | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C, H | Heavy chain | protein | 216 | 6% helix, 52% strand | — |
| D | Light chain | protein | 215 | 6% helix, 50% strand | — |
| E | MHC class I antigen | protein | 275 | 25% helix, 40% strand | F6IQY1 |
| L | Light chain | protein | 216 | 6% helix, 52% strand | — |
| T, U | Peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, L, B, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.78 | 0.84 | 82 | empty |
| 2 | 574 | 0.78 | 0.85 | 73 | empty |
| 3 | 460 | 0.70 | 0.80 | 51 | PEG, GOL |
| 4 | 451 | 0.69 | 0.80 | 43 | GOL, PEG |
| 5 | 252 | 0.60 | 0.80 | 32 | empty |
Interfaces
13 interfaces between chains.
- C–D · 1608 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1565 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1317 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1301 Ų buried · 19 hydrogen bonds · protein-protein
- E–T · 919 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6ID4 · Defining the structural basis for human alloantibody binding to human leukocyte antigen… · the same entry in another collection · chain U against U, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 F6IQY1
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6ID4 · PDBe 6ID4 · UniProt F6IQY1 · UniProt P61769
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