MolNFT v1 · #74877 · protein
Crystal structure of H2-kb in complex with a mutant of the chicken ovalbumin epitope ova-G4
3P9M · H-2 class I histocompatibility antigen, K-B alpha chain: “Crystal structure of H2-kb in complex with a mutant of the chicken ovalbumin epitope ova-G4”. X-ray diffraction, 10 pockets (best druggability 0.65). MolNFT v1 #74877 on…
- PDB
- 3P9M
- Type
- protein
- Length
- 768 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; Ovalbumin…
- UniProt
- P01901, P01887, P01012
- Pockets
- 10 · best druggability 0.65
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 | 277 | 28% helix, 39% strand | P01901 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F | Ovalbumin epitope, siigfekl | protein | 8 | 0% helix, 0% strand | P01012 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.65 | 0.75 | 58 | empty |
| 2 | 685 | 0.64 | 0.74 | 61 | empty |
| 3 | 163 | 0.51 | 0.79 | 29 | empty |
| 4 | 136 | 0.51 | 0.80 | 26 | empty |
| 5 | 130 | 0.49 | 0.79 | 21 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1199 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1196 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 843 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 838 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 649 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3P9M · Crystal Structure of H2-Kb in complex with a mutant of the chicken ovalbumin epitope… · the same entry in another collection · chain F against F, 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
- P01012 · AlphaFold monomer V2.0 prediction for ovalbumin (P01012) · a predicted model of the same protein · chain C against A, TM-score 0.54
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 P01012
- Elsewhere: RCSB PDB 3P9M · PDBe 3P9M · UniProt P01901 · UniProt P01887 · UniProt P01012
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