MolNFT v1 · #155559 · protein
Crystal structure of bony fish MHC class I binding BETA2M-2 for 2.6 ångström
6LBE · MHC class I antigen: “Crystal structure of bony fish MHC class I binding BETA2M-2 for 2.6 ångström”. X-ray diffraction, 5 pockets (best druggability 0.76). MolNFT v1 #155559 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6LBE
- Type
- protein
- Length
- 756 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; 9-mer peptide from RNA-directed RNA polymerase…
- UniProt
- Q65XY8, A0A3G2VUI3
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 274 | 29% helix, 39% strand | Q65XY8 |
| B, D | Beta-2-microglobulin | protein | 98 | 0% helix, 51% strand | A0A3G2VUI3 |
| C | MHC class I antigen | protein | 268 | 27% helix, 41% strand | Q65XY8 |
| E, F | 9-mer peptide from RNA-directed RNA polymerase L | protein | 9 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.76 | 0.78 | 109 | empty |
| 2 | 760 | 0.72 | 0.78 | 63 | empty |
| 3 | 500 | 0.67 | 0.78 | 45 | empty |
| 4 | 494 | 0.67 | 0.78 | 53 | empty |
| 5 | 88 | 0.57 | 0.87 | 19 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1838 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1725 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 887 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 883 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 213 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6LBE · Crystal structure of bony fish MHC class I binding beta2M-2 for 2.6 angstrom · the same entry in another collection · chain A against A, TM-score 1.00
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 Q65XY8
- Every structure of UniProt A0A3G2VUI3
- Elsewhere: RCSB PDB 6LBE · PDBe 6LBE · UniProt Q65XY8 · UniProt A0A3G2VUI3
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