Research workbench
Crystal structure of MHC-like MILL2
Analyse Crystal structure of MHC-like MILL2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A97
- Type
- protein
- Length
- 687 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC I-like leukocyte 2 long form; Beta-2-microglobulin
- UniProt
- Q8HWE5, P01887
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC I-like leukocyte 2 long form | protein | 267 | 24% helix, 42% strand | Q8HWE5 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P01887 |
| C | MHC I-like leukocyte 2 long form | protein | 225 | 22% helix, 44% strand | Q8HWE5 |
| D | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | P01887 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.68 | 0.95 | 19 | SO4 |
| 2 | 393 | 0.65 | 0.79 | 42 | empty |
| 3 | 417 | 0.59 | 0.75 | 47 | empty |
| 4 | 97 | 0.53 | 0.84 | 23 | empty |
| 5 | 252 | 0.53 | 0.76 | 34 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1346 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 666 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 614 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 587 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6A97 · Crystal structure of MHC-like MILL2 · the same entry in another collection · chain D against D, 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
- Q8HWE5 · AlphaFold monomer V2.0 prediction for MHC class I-like protein MILL2 (Q8HWE5) · a predicted model of the same protein · chain C against A, TM-score 0.68
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 Q8HWE5
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 6A97 · PDBe 6A97 · UniProt Q8HWE5 · UniProt P01887
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