Research workbench
Crystal structure of BM3.3 scfv TCR in complex with PBM8-H-2KBM8 MHC class I molecule
Analyse Crystal structure of BM3.3 scfv TCR in complex with PBM8-H-2KBM8 MHC class I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OL3
- Type
- protein
- Length
- 615 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BM3.3 T-cell receptor alpha-chain; BM3.3 T-cell receptor beta-chain; Allogeneic H-2KBM8…
- UniProt
- Q5R1F1, P04214, P01901, P01887, Q91YE7
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BM3.3 T-cell receptor alpha-chain | protein | 118 | 3% helix, 44% strand | Q5R1F1 |
| B | BM3.3 T-cell receptor beta-chain | protein | 113 | 0% helix, 58% strand | P04214 |
| H | Allogeneic H-2KBM8 MHC class I molecule | protein | 276 | 27% helix, 38% strand | P01901 |
| L | Beta-2-microglobulin | protein | 100 | 0% helix, 45% strand | P01887 |
| P | Naturally processed octapeptide PBM8 | protein | 8 | 0% helix, 0% strand | Q91YE7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.63 | 0.75 | 55 | empty |
| 2 | 137 | 0.59 | 0.84 | 29 | empty |
| 3 | 84 | 0.51 | 0.83 | 21 | empty |
| 4 | 168 | 0.49 | 0.77 | 25 | empty |
| 5 | 143 | 0.44 | 0.76 | 30 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1258 Ų buried · 21 hydrogen bonds · protein-protein
- H–P · 913 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 845 Ų buried · 14 hydrogen bonds · protein-protein
- B–H · 366 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 362 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2OL3 · crystal structure of BM3.3 ScFV TCR in complex with PBM8-H-2KBM8 MHC class I molecule · the same entry in another collection · chain P against P, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain L against A, TM-score 0.99
- P04214 · AlphaFold monomer V2.0 prediction for T-cell receptor beta chain V region E1 (P04214) · a predicted model of the same protein · chain B against A, TM-score 0.96
- Q91YE7 · AlphaFold monomer V2.0 prediction for RNA-binding protein 5 (Q91YE7) · a predicted model of the same protein · chain P against A, TM-score 0.47
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 Q5R1F1
- Every structure of UniProt P04214
- Every structure of UniProt P01901
- Every structure of UniProt P01887
- Every structure of UniProt Q91YE7
- Elsewhere: RCSB PDB 2OL3 · PDBe 2OL3 · UniProt Q5R1F1 · UniProt P04214 · UniProt P01901 · UniProt P01887 · UniProt Q91YE7
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