Research workbench
V BETA/V beta homodimerization-based pre-TCR model suggested by TCR beta crystal structures
Analyse V BETA/V beta homodimerization-based pre-TCR model suggested by TCR beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q5Y
- Type
- protein
- Length
- 955 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TCR N15 beta
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TCR N15 beta | protein | 240 | 7% helix, 52% strand | — |
| B, D | TCR N15 beta | protein | 238 | 7% helix, 52% strand | — |
| C | TCR N15 beta | protein | 239 | 7% helix, 52% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.85 | 0.86 | 112 | GOL, PEG, EPE |
| 2 | 711 | 0.75 | 0.80 | 66 | GOL |
| 3 | 556 | 0.73 | 0.81 | 44 | empty |
| 4 | 383 | 0.72 | 0.83 | 42 | empty |
| 5 | 325 | 0.60 | 0.78 | 40 | GOL |
Interfaces
5 interfaces between chains.
- C–D · 1316 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1236 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1193 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 116 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3Q5Y · V beta/V beta homodimerization-based pre-TCR model suggested by TCR beta crystal… · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 3Q5Y · PDBe 3Q5Y
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