Research workbench
Crystal structure of the major histocompatibility complex class I H- 2KB molecule containing a single viral peptide: implications for peptide binding and T-cell receptor recognition
Analyse Crystal structure of the major histocompatibility complex class I H- 2KB… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2MHA
- Type
- protein
- Length
- 754 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class I histocompatibility antigen (H-2KB) (alpha chain); Beta 2-microglobulin; Viral…
- UniProt
- P01901, P01887, P11212
- Pockets
- 10 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Class I histocompatibility antigen (H-2KB) (alpha chain) | protein | 270 | 24% helix, 37% strand | P01901 |
| B, D | Beta 2-microglobulin | protein | 99 | 3% helix, 40% strand | P01887 |
| E, F | Viral octapeptide arg-gly-tyr-val-tyr-gln-gly-leu | protein | 8 | 0% helix, 0% strand | P11212 |
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.59 | 0.74 | 39 | empty |
| 2 | 450 | 0.57 | 0.74 | 43 | empty |
| 3 | 141 | 0.46 | 0.77 | 27 | empty |
| 4 | 142 | 0.44 | 0.76 | 30 | empty |
| 5 | 64 | 0.42 | 0.82 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1223 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1218 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 903 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 858 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 184 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2MHA · Crystal structure of the major histocompatibility complex class I H-2KB molecule… · 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 0.98
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 P01887
- Every structure of UniProt P11212
- Elsewhere: RCSB PDB 2MHA · PDBe 2MHA · UniProt P01901 · UniProt P01887 · UniProt P11212
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