MolNFT v1 · #96719 · protein
Crystal structure of CA5 TCR-HLA B*3505-lpep complex
4JRX · MHC class I antigen: “Crystal structure of CA5 TCR-HLA B*3505-lpep complex”. X-ray diffraction, 2 ligands (NA, IOD), 10 pockets (best druggability 0.75). MolNFT v1 #96719 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4JRX
- Type
- protein
- Length
- 830 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Trans-activator protein BZLF1; CA5 TCR alpha…
- UniProt
- C5MK56, P61769, Q3KSS8
- Ligands
- NA, IOD
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 27% helix, 39% strand | C5MK56 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Trans-activator protein BZLF1 | protein | 13 | 0% helix, 8% strand | Q3KSS8 |
| D | CA5 TCR alpha chain | protein | 204 | 3% helix, 44% strand | — |
| E | CA5 TCR beta chain | protein | 238 | 8% helix, 50% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, D, E
- IOD · Iodide ion · ion · 8 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.75 | 0.78 | 74 | NA, IOD |
| 2 | 567 | 0.68 | 0.78 | 54 | empty |
| 3 | 68 | 0.62 | 0.91 | 22 | IOD |
| 4 | 112 | 0.45 | 0.78 | 24 | empty |
| 5 | 73 | 0.37 | 0.78 | 15 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2364 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1288 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 981 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 477 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 282 Ų buried · 8 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 C5MK56
- Every structure of UniProt P61769
- Every structure of UniProt Q3KSS8
- Elsewhere: RCSB PDB 4JRX · PDBe 4JRX · UniProt C5MK56 · UniProt P61769 · UniProt Q3KSS8
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