Research workbench
Conformational switch in polymorphic H-2K molecules containing an HSV peptide
Analyse Conformational switch in polymorphic H-2K molecules containing an HSV peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T0M
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- 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…
- UniProt
- P01901, P01887, P06436
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 278 | 28% helix, 38% strand | P01901 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| P, Q | Glycoprotein B | protein | 8 | 0% helix, 0% strand | P06436 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.68 | 0.75 | 60 | empty |
| 2 | 561 | 0.63 | 0.75 | 50 | empty |
| 3 | 134 | 0.42 | 0.75 | 27 | empty |
| 4 | 127 | 0.41 | 0.75 | 27 | empty |
| 5 | 80 | 0.40 | 0.78 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1246 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1241 Ų buried · 20 hydrogen bonds · protein-protein
- D–Q · 844 Ų buried · 20 hydrogen bonds · protein-protein
- A–P · 843 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 366 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1T0M · Conformational switch in polymorphic H-2K molecules containing an HSV peptide · the same entry in another collection · chain Q against Q, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P01887
- Every structure of UniProt P06436
- Elsewhere: RCSB PDB 1T0M · PDBe 1T0M · UniProt P01901 · UniProt P01887 · UniProt P06436
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