Research workbench
Crystal structure of macrophage migration inhibitory factor bound to an acetaminophen dimer derived from napqi
Analyse Crystal structure of macrophage migration inhibitory factor bound to an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DJI
- Type
- protein
- Length
- 684 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage migration inhibitory factor
- EC
- 5.3.2.1
- UniProt
- P14174
- Ligands
- 3E1, CL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Macrophage migration inhibitory factor (EC 5.3.2.1) | protein | 114 | 39% helix, 31% strand | P14174 |
Ligands and binding sites
- 3E1 · N,N'-(6,6'-dihydroxybiphenyl-3,3'-diyl)diacetamide · ligand · chains A, B
- CL · Chloride ion · ion · 15 copies · chains A, C, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.85 | 0.93 | 43 | empty |
| 2 | 412 | 0.82 | 0.90 | 50 | empty |
| 3 | 57 | 0.48 | 0.85 | 13 | empty |
| 4 | 154 | 0.44 | 0.75 | 18 | CL |
| 5 | 58 | 0.42 | 0.81 | 13 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1210 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 1191 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1161 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1150 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1146 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3DJI · Crystal Structure of Macrophage Migration Inhibitory Factor Bound to an Acetaminophen… · 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 P14174
- Elsewhere: RCSB PDB 3DJI · PDBe 3DJI · UniProt P14174
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