Research workbench
Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR B3K506
Analyse Crystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C5Z
- Type
- protein
- Length
- 1,651 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.55
- Source
- Mus musculus
- Molecule
- TCR B3K506 Alpha Chain; TCR B3K506 Beta Chain; H-2 class II histocompatibility antigen…
- UniProt
- P14434, P14483
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.55 · 5 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TCR B3K506 Alpha Chain | protein | 202 | 3% helix, 44% strand | — |
| B, F | TCR B3K506 Beta Chain | protein | 240 | 7% helix, 50% strand | — |
| C, G | H-2 class II histocompatibility antigen, A-B alpha chain | protein | 182 | 14% helix, 44% strand | P14434 |
| D, H | 3K peptide, Linker, and H-2 class II histocompatibility antigen (A beta chain) | protein | 202 | 20% helix, 44% strand | P14483 |
| E | TCR B3K506 Alpha Chain | protein | 201 | 3% helix, 45% strand | — |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.74 | 0.97 | 20 | empty |
| 2 | 1125 | 0.72 | 0.76 | 83 | empty |
| 3 | 1006 | 0.71 | 0.76 | 66 | empty |
| 4 | 993 | 0.70 | 0.75 | 63 | empty |
| 5 | 962 | 0.70 | 0.75 | 68 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3001 Ų buried · 53 hydrogen bonds · protein-protein
- G–H · 2995 Ų buried · 53 hydrogen bonds · protein-protein
- E–F · 2220 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2180 Ų buried · 21 hydrogen bonds · protein-protein
- D–H · 763 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3C5Z · Crystal structure of mouse MHC class II I-AB/3K peptide complexed with mouse TCR B3K506 · the same entry in another collection · chain H against H, 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 0.75
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 3C5Z · PDBe 3C5Z · UniProt P14434 · UniProt P14483
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