Research workbench
Structure of apomif
Analyse Structure of apomif in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GAD
- Type
- protein
- Length
- 696 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage migration inhibitory factor-like protein
- UniProt
- Q1HEA2
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Macrophage migration inhibitory factor-like protein | protein | 115 | 41% helix, 30% strand | Q1HEA2 |
| C, E, F | Macrophage migration inhibitory factor-like protein | protein | 117 | 40% helix, 29% strand | Q1HEA2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, E, F, C, D
- ACY · Acetic acid · additive · 4 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.76 | 0.99 | 29 | empty |
| 2 | 80 | 0.75 | 0.97 | 28 | empty |
| 3 | 546 | 0.66 | 0.77 | 64 | empty |
| 4 | 201 | 0.48 | 0.75 | 33 | empty |
| 5 | 82 | 0.43 | 0.79 | 17 | SO4, ACY |
Interfaces
10 interfaces between chains.
- E–F · 1417 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1410 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1353 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 1336 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1334 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3GAD · Structure of apomif · the same entry in another collection · chain A against A, 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 Q1HEA2
- Elsewhere: RCSB PDB 3GAD · PDBe 3GAD · UniProt Q1HEA2
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