MolNFT v1 · #139744 · protein
Crystal structure of phla-B35 in complex with TU55 T cell receptor
5XOT · HLA class I histocompatibility antigen, B-35 alpha chain: “Crystal structure of phla-B35 in complex with TU55 T cell receptor”. X-ray diffraction, 14 pockets (best druggability 0.75). MolNFT v1 #139744 on GenesisL1: 3D structure…
- PDB
- 5XOT
- Type
- protein
- Length
- 829 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-35 alpha chain; Beta-2-microglobulin; An HIV…
- UniProt
- P30685, P61769
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-35 alpha chain | protein | 276 | 29% helix, 39% strand | P30685 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | An HIV reverse transcriptase epitope | protein | 9 | 0% helix, 0% strand | — |
| D | The delta chain of TU55 TCR | protein | 203 | 4% helix, 45% strand | — |
| E | The beta chain of TU55 TCR | protein | 242 | 7% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.75 | 0.78 | 75 | empty |
| 2 | 160 | 0.74 | 0.92 | 27 | empty |
| 3 | 615 | 0.70 | 0.79 | 48 | GOL |
| 4 | 129 | 0.51 | 0.80 | 23 | GOL |
| 5 | 228 | 0.50 | 0.75 | 43 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2329 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1382 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 862 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 470 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 413 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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 P30685
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5XOT · PDBe 5XOT · UniProt P30685 · UniProt P61769
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