Research workbench
TCR55 in complex with HIV(Pol448-456)/HLA-B35
Analyse TCR55 in complex with HIV(Pol448-456)/HLA-B35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BJ3
- Type
- protein
- Length
- 826 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.898
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- HLA class I histocompatibility antigen, B-35 alpha chain; Beta-2-microglobulin; TCR 55…
- UniProt
- P30685, P61769, Q6IRV4, K7N5M4
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · resolution 1.898 · 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 | 275 | 28% helix, 39% strand | P30685 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| D | TCR 55 alpha chain | protein | 202 | 5% helix, 43% strand | Q6IRV4 |
| H | TCR 55 beta chain | protein | 241 | 8% helix, 49% strand | K7N5M4 |
| C | HIV Pol B35 peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, D, H
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.75 | 0.78 | 82 | SO4 |
| 2 | 82 | 0.75 | 0.97 | 23 | EDO |
| 3 | 561 | 0.69 | 0.79 | 45 | empty |
| 4 | 290 | 0.54 | 0.75 | 38 | empty |
| 5 | 118 | 0.46 | 0.79 | 23 | empty |
Interfaces
7 interfaces between chains.
- D–H · 2335 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1324 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 849 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 504 Ų buried · 5 hydrogen bonds · protein-protein
- A–H · 374 Ų buried · 4 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
- Every structure of UniProt Q6IRV4
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 6BJ3 · PDBe 6BJ3 · UniProt P30685 · UniProt P61769 · UniProt Q6IRV4 · UniProt K7N5M4
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