MolNFT v1 · #13529 · protein
Crystal structure of H-2KBM3 bound to DEV8
1LEK · H-2 class I histocompatibility antigen, K-B alpha chain: “Crystal structure of H-2KBM3 bound to DEV8”. X-ray diffraction, 3 ligands (NAG, FUC, PO4), 6 pockets (best druggability 0.61). MolNFT v1 #13529 on GenesisL1: 3D structure…
- PDB
- 1LEK
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin; DEV8
- UniProt
- P01901, P01887
- Ligands
- NAG, FUC, PO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 274 | 29% helix, 39% strand | P01901 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 53% strand | P01887 |
| P | DEV8 | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.61 | 0.80 | 43 | PO4 |
| 2 | 257 | 0.54 | 0.76 | 31 | empty |
| 3 | 65 | 0.52 | 0.86 | 17 | empty |
| 4 | 116 | 0.49 | 0.80 | 23 | empty |
| 5 | 61 | 0.31 | 0.75 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1346 Ų buried · 25 hydrogen bonds · protein-protein
- A–P · 891 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, oxidation).
Compared structures
- 1LEK · Crystal Structure of H-2Kbm3 bound to dEV8 · the same entry in another collection · chain A against A, TM-score 1.00
- P01901 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, K-B alpha… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · 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 P01901
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 1LEK · PDBe 1LEK · UniProt P01901 · UniProt P01887
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