Research workbench
6235 TCR bound to I-ab PADI4
Analyse 6235 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
- 6MNO
- Type
- protein
- Length
- 802 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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
- 9 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | H-2 class II histocompatibility antigen, a-B alpha chain | protein | 174 | 12% helix, 42% strand | P14434 |
| D | PADI4 (92-105) peptide and MHC class II I-ab beta chain (EC 3.5.3.15) | protein | 193 | 21% helix, 44% strand | Q9Z183, P14483 |
| A | 6235 TCR alpha chain | protein | 196 | 3% helix, 44% strand | — |
| B | 6235 TCR beta chain | protein | 239 | 7% helix, 51% strand | — |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.74 | 0.77 | 97 | empty |
| 2 | 272 | 0.66 | 0.83 | 43 | empty |
| 3 | 160 | 0.51 | 0.79 | 22 | empty |
| 4 | 164 | 0.44 | 0.74 | 25 | empty |
| 5 | 136 | 0.42 | 0.75 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2900 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2064 Ų buried · 22 hydrogen bonds · protein-protein
- C–B · 404 Ų buried · 5 hydrogen bonds · protein-protein
- D–A · 211 Ų buried · 5 hydrogen bonds · protein-protein
- D–B · 196 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6MNO · 6235 TCR bound to I-Ab Padi4 · the same entry in another collection · chain C against C, 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 0.95
- 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 6MNO · PDBe 6MNO · UniProt P14434 · UniProt Q9Z183 · UniProt P14483
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