Research workbench
Crystal structure of murine P14 TCR complex with H-2DB and Y4A, modified GP33 peptide from lcmv
Analyse Crystal structure of murine P14 TCR complex with H-2DB and Y4A, modified GP33… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M00
- Type
- protein
- Length
- 810 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin; Protein…
- UniProt
- P01899, P01887, A0A0G2JF94, Q6PIR9, P04213, Q7TND8
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 276 | 28% helix, 39% strand | P01899 |
| B | Beta-2-microglobulin | protein | 101 | 0% helix, 49% strand | P01887 |
| G | Protein TRAV14-1,UNCHARACTERIZED protein | protein | 187 | 4% helix, 47% strand | A0A0G2JF94, Q6PIR9 |
| H | T-cell receptor beta chain V region C5,UNCHARACTERIZED protein | protein | 237 | 7% helix, 54% strand | P04213, Q7TND8 |
| P | Lcmv-derived GP33 altered peptide ligand Y4A | protein | 9 | 0% helix, 0% strand | — |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.73 | 0.77 | 70 | empty |
| 2 | 573 | 0.63 | 0.75 | 50 | empty |
| 3 | 174 | 0.54 | 0.79 | 32 | empty |
| 4 | 147 | 0.52 | 0.80 | 29 | empty |
| 5 | 168 | 0.51 | 0.78 | 35 | empty |
Interfaces
7 interfaces between chains.
- G–H · 2231 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1436 Ų buried · 23 hydrogen bonds · protein-protein
- A–P · 896 Ų buried · 23 hydrogen bonds · protein-protein
- A–G · 446 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 369 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5M00 · Crystal structure of murine P14 TCR complex with H-2Db and Y4A, modified gp33 peptide… · the same entry in another collection · chain B against B, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P04213 · AlphaFold monomer V2.0 prediction for T-cell receptor beta chain V region C5 (P04213) · a predicted model of the same protein · chain H against A, TM-score 0.46
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 P01899
- Every structure of UniProt P01887
- Every structure of UniProt A0A0G2JF94
- Every structure of UniProt Q6PIR9
- Every structure of UniProt P04213
- Every structure of UniProt Q7TND8
- Elsewhere: RCSB PDB 5M00 · PDBe 5M00 · UniProt P01899 · UniProt P01887 · UniProt A0A0G2JF94 · UniProt Q6PIR9 · UniProt P04213 · UniProt Q7TND8
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