MolNFT v1 · #116076 · protein
Crystal structure of C25-nlv-HLA-A2 complex
5D2N · C25 alpha: “Crystal structure of C25-nlv-HLA-A2 complex”. X-ray diffraction, 18 pockets (best druggability 0.79). MolNFT v1 #116076 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5D2N
- Type
- protein
- Length
- 1,651 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C25 alpha; C25 beta; HLA class I histocompatibility antigen, a-2 alpha chain…
- UniProt
- P01892, P61769
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | C25 alpha | protein | 198 | 5% helix, 43% strand | — |
| F | C25 beta | protein | 246 | 7% helix, 48% strand | — |
| H, A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 273 | 27% helix, 41% strand | P01892 |
| L, B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| E | C25 beta | protein | 245 | 7% helix, 48% strand | — |
| G, I | Asn-leu-val-pro-met-val-ala-thr-val | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- IMD · Imidazole · additive · 3 copies · chains C, A, B
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 | 957 | 0.79 | 0.81 | 108 | empty |
| 2 | 972 | 0.77 | 0.79 | 72 | empty |
| 3 | 720 | 0.74 | 0.80 | 92 | empty |
| 4 | 502 | 0.70 | 0.80 | 83 | empty |
| 5 | 698 | 0.69 | 0.76 | 58 | empty |
Interfaces
21 interfaces between chains.
- D–E · 2140 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 2133 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1366 Ų buried · 25 hydrogen bonds · protein-protein
- H–L · 1340 Ų buried · 19 hydrogen bonds · protein-protein
- H–G · 815 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5D2N · PDBe 5D2N · UniProt P01892 · UniProt P61769
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.