Research workbench
Structure of human melanoma inhibitory activity (mia) protein in complex with pyrimidin-2-amine
Analyse Structure of human melanoma inhibitory activity (mia) protein in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IXB
- Type
- protein
- Length
- 210 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Melanoma-derived growth regulatory protein
- UniProt
- Q16674
- Ligands
- LGA
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Melanoma-derived growth regulatory protein | protein | 105 | 10% helix, 40% strand | Q16674 |
Ligands and binding sites
- LGA · Pyrimidin-2-amine · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.57 | 0.87 | 19 | LGA |
| 2 | 72 | 0.53 | 0.86 | 20 | LGA |
| 3 | 188 | 0.48 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 227 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5IXB · Structure of human Melanoma Inhibitory Activity (MIA) Protein in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q16674 · AlphaFold monomer V2.0 prediction for melanoma-derived growth regulatory protein (Q16674) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q16674
- Elsewhere: RCSB PDB 5IXB · PDBe 5IXB · UniProt Q16674
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