Research workbench
TCR589 in complex with HIV(POL448-456)/HLA-B35
Analyse TCR589 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
- 6BJ2
- Type
- protein
- Length
- 824 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TCR 589 alpha chain; TCR 589 beta chain; HLA class I histocompatibility antigen, B-35…
- UniProt
- Q6IRV4, K7N5M4, P30685, P61769
- Ligands
- NAG, ZN
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | TCR 589 alpha chain | protein | 203 | 3% helix, 40% strand | Q6IRV4 |
| E | TCR 589 beta chain | protein | 241 | 6% helix, 48% strand | K7N5M4 |
| A | HLA class I histocompatibility antigen, B-35 alpha chain | protein | 273 | 25% helix, 38% strand | P30685 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P61769 |
| C | HIV pol B35 peptide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains D, E
- ZN · Zinc ion · metal · 3 copies · chains D, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.75 | 0.77 | 80 | empty |
| 2 | 529 | 0.67 | 0.78 | 51 | empty |
| 3 | 81 | 0.46 | 0.82 | 17 | empty |
| 4 | 154 | 0.46 | 0.76 | 23 | empty |
| 5 | 109 | 0.45 | 0.79 | 25 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2180 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1172 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 870 Ų buried · 13 hydrogen bonds · protein-protein
- D–A · 592 Ų buried · 13 hydrogen bonds · protein-protein
- E–A · 384 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
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 Q6IRV4
- Every structure of UniProt K7N5M4
- Every structure of UniProt P30685
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6BJ2 · PDBe 6BJ2 · UniProt Q6IRV4 · UniProt K7N5M4 · UniProt P30685 · UniProt P61769
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