MolNFT v1 · #149808 · protein
Structure of H-2KB with dipeptide gl
6GB6 · H-2 class I histocompatibility antigen, K-B alpha chain: “Structure of H-2KB with dipeptide gl”. X-ray diffraction, 11 pockets (best druggability 0.63). MolNFT v1 #149808 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GB6
- Type
- protein
- Length
- 753 residues
- Chains
- 4
- 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
- UniProt
- P01901, P01887
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 275 | 24% helix, 39% strand | P01901 |
| D | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 278 | 28% helix, 39% strand | P01901 |
| E, B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P01887 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.63 | 0.74 | 51 | GOL |
| 2 | 273 | 0.62 | 0.80 | 31 | GOL |
| 3 | 283 | 0.62 | 0.79 | 29 | empty |
| 4 | 550 | 0.61 | 0.74 | 51 | GOL |
| 5 | 336 | 0.59 | 0.77 | 62 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1255 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1226 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 280 Ų buried · 6 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 P01901
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 6GB6 · PDBe 6GB6 · UniProt P01901 · UniProt P01887
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