Research workbench
4699 TCR bound to I-Ab Padi4
Analyse 4699 TCR bound to I-Ab Padi4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MKD
- Type
- protein
- Length
- 799 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Mus musculus
- Molecule
- H-2 class II histocompatibility antigen, A-B alpha chain; Padi4 (92-105) peptide and MHC…
- EC
- 3.5.3.15
- UniProt
- P14434, Q9Z183, P14483
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · resolution 3.2 · 4 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | H-2 class II histocompatibility antigen, A-B alpha chain | protein | 166 | 16% helix, 39% strand | P14434 |
| D | Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain (EC 3.5.3.15) | protein | 201 | 17% helix, 40% strand | Q9Z183, P14483 |
| A | 4699 TCR alpha chain | protein | 193 | 5% helix, 42% strand | — |
| B | 4699 TCR beta chain | protein | 239 | 6% helix, 49% strand | — |
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.66 | 0.83 | 43 | empty |
| 2 | 428 | 0.58 | 0.74 | 49 | empty |
| 3 | 269 | 0.52 | 0.75 | 42 | empty |
| 4 | 149 | 0.48 | 0.77 | 21 | empty |
| 5 | 184 | 0.46 | 0.75 | 33 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2923 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 1785 Ų buried · 22 hydrogen bonds · protein-protein
- C–B · 419 Ų buried · 6 hydrogen bonds · protein-protein
- D–A · 193 Ų buried · 5 hydrogen bonds · protein-protein
- D–B · 186 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6MKD · 4699 TCR bound to I-ab PADI4 · the same entry in another collection · chain A against A, TM-score 1.00
- P14434 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-B alpha… · a predicted model of the same protein · chain C against A, TM-score 0.94
- P14483 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a beta… · a predicted model of the same protein · chain D against A, TM-score 0.74
- Q9Z183 · AlphaFold monomer V2.0 prediction for protein-arginine deiminase type-4 (Q9Z183) · a predicted model of the same protein · chain D against A, TM-score 0.40
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 P14434
- Every structure of UniProt Q9Z183
- Every structure of UniProt P14483
- Elsewhere: RCSB PDB 6MKD · PDBe 6MKD · UniProt P14434 · UniProt Q9Z183 · UniProt P14483
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.