Research workbench
Crystal structure of the murine class I major histocompatibility complex of H-2DB, B2-microglobulin, and a 9-residue peptide derived from rat dopamine beta-monooxigenase
Analyse Crystal structure of the murine class I major histocompatibility complex of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZHB
- Type
- protein
- Length
- 1,524 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin; 9-mer…
- EC
- 1.14.17.1
- UniProt
- P01899, P01887, Q05754
- Pockets
- 19 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 273 | 26% helix, 41% strand | P01899 |
| B, E, H, K | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F, I, L | 9-mer peptide from dopamine beta-monooxygenase (EC 1.14.17.1) | protein | 9 | 0% helix, 0% strand | Q05754 |
Pockets
19 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.68 | 0.78 | 59 | empty |
| 2 | 561 | 0.68 | 0.78 | 55 | empty |
| 3 | 661 | 0.67 | 0.76 | 54 | empty |
| 4 | 654 | 0.67 | 0.76 | 57 | empty |
| 5 | 137 | 0.49 | 0.79 | 27 | empty |
Interfaces
10 interfaces between chains.
- J–K · 1366 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1364 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1364 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1357 Ų buried · 17 hydrogen bonds · protein-protein
- G–I · 960 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1ZHB · Crystal Structure Of The Murine Class I Major Histocompatibility Complex Of H-2Db… · the same entry in another collection · chain L against L, TM-score 1.00
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 P01899
- Every structure of UniProt P01887
- Every structure of UniProt Q05754
- Elsewhere: RCSB PDB 1ZHB · PDBe 1ZHB · UniProt P01899 · UniProt P01887 · UniProt Q05754
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