Research workbench
Crystal structure of the RL42 TCR in complex with HLA-B8-flr
Analyse Crystal structure of the RL42 TCR in complex with HLA-B8-flr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SJV
- Type
- protein
- Length
- 3,293 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-8 alpha chain; Beta-2-microglobulin…
- UniProt
- P30460, P61769, Q3KST2
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 8% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, K, P | HLA class I histocompatibility antigen, B-8 alpha chain | protein | 277 | 25% helix, 19% strand | P30460 |
| B, G | Beta-2-microglobulin | protein | 99 | 0% helix, 38% strand | P61769 |
| C, H, M, R | Epstein-barr nuclear antigen 3 | protein | 9 | 0% helix, 0% strand | Q3KST2 |
| D, I, N, S | RL42 T cell receptor, alpha chain | protein | 197 | 0% helix, 34% strand | — |
| E, O, T | RL42 T cell receptor, beta chain | protein | 241 | 5% helix, 46% strand | — |
| J | RL42 T cell receptor, beta chain | protein | 240 | 4% helix, 45% strand | — |
| L, Q | Beta-2-microglobulin | protein | 100 | 0% helix, 24% strand | P61769 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.79 | 0.81 | 106 | empty |
| 2 | 867 | 0.77 | 0.80 | 94 | empty |
| 3 | 1081 | 0.72 | 0.76 | 89 | empty |
| 4 | 1195 | 0.71 | 0.75 | 99 | empty |
| 5 | 599 | 0.70 | 0.79 | 57 | empty |
Interfaces
42 interfaces between chains.
- N–O · 2257 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2239 Ų buried · 25 hydrogen bonds · protein-protein
- I–J · 2226 Ų buried · 25 hydrogen bonds · protein-protein
- S–T · 2122 Ų buried · 26 hydrogen bonds · protein-protein
- P–Q · 1431 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 disulfide (disulfide).
Compared structures
- 3SJV · Crystal structure of the RL42 TCR in complex with HLA-B8-FLR · the same entry in another collection · chain T against T, TM-score 1.00
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 P30460
- Every structure of UniProt P61769
- Every structure of UniProt Q3KST2
- Elsewhere: RCSB PDB 3SJV · PDBe 3SJV · UniProt P30460 · UniProt P61769 · UniProt Q3KST2
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