Research workbench
Crystal structure of the lcmv derived peptide GP34 in complex with the murine MHC class I H-2 kb
Analyse Crystal structure of the lcmv derived peptide GP34 in complex with the murine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TID
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin; Lcmv…
- UniProt
- P01901, P61769
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 277 | 28% helix, 39% strand | P01901 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Lcmv derived octamer peptide | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.65 | 0.75 | 57 | ACT |
| 2 | 73 | 0.36 | 0.77 | 16 | empty |
| 3 | 73 | 0.33 | 0.75 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1293 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 813 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3TID · Crystal structure of the LCMV derived peptide GP34 in complex with the murine mhc class I… · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P01901
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3TID · PDBe 3TID · UniProt P01901 · UniProt P61769
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