MolNFT v1 · #103037 · protein
J809.B5 Y31A TCR bound to IAB3K
4P46 · H-2 class II histocompatibility antigen, a-B alpha chain: “J809.B5 Y31A TCR bound to IAB3K”. X-ray diffraction, 10 pockets (best druggability 0.70). MolNFT v1 #103037 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4P46
- Type
- protein
- Length
- 815 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; 3K PEPTIDE,H-2 class II…
- UniProt
- P14434, P14483
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | H-2 class II histocompatibility antigen, a-B alpha chain | protein | 179 | 13% helix, 45% strand | P14434 |
| D | 3K PEPTIDE,H-2 class II histocompatibility antigen, a beta chain | protein | 199 | 19% helix, 43% strand | P14483 |
| A | J809.B5 TCR Y31A alpha chain (VA2.8) | protein | 199 | 2% helix, 46% strand | — |
| B | J809.B5 TCR beta chain (VB8.2) | protein | 238 | 6% helix, 51% strand | — |
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 | 997 | 0.70 | 0.74 | 78 | empty |
| 2 | 93 | 0.58 | 0.87 | 26 | empty |
| 3 | 192 | 0.51 | 0.78 | 26 | empty |
| 4 | 189 | 0.48 | 0.75 | 28 | empty |
| 5 | 146 | 0.46 | 0.76 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2813 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2019 Ų buried · 22 hydrogen bonds · protein-protein
- C–B · 423 Ų buried · 7 hydrogen bonds · protein-protein
- D–B · 290 Ų buried · 5 hydrogen bonds · protein-protein
- D–A · 193 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4P46 · J809.B5 Y31A TCR bound to IAb3K · 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
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 P14483
- Elsewhere: RCSB PDB 4P46 · PDBe 4P46 · UniProt P14434 · UniProt P14483
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