Research workbench
Crystal structure analysis of macrophage migration inhibitory factor in complex with dimethylformamide
Analyse Crystal structure analysis of macrophage migration inhibitory factor in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P0H
- Type
- protein
- Length
- 341 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage migration inhibitory factor
- EC
- 5.3.2.1, 5.3.3.12
- UniProt
- P14174
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 113 | 39% helix, 31% strand | P14174 |
| B, C | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 114 | 39% helix, 31% strand | P14174 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.85 | 0.91 | 53 | empty |
| 2 | 89 | 0.54 | 0.84 | 13 | DMF |
| 3 | 69 | 0.50 | 0.84 | 15 | DMF |
| 4 | 65 | 0.42 | 0.80 | 16 | DMF |
| 5 | 121 | 0.37 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1139 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1120 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1106 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct).
Compared structures
- 4P0H · Crystal Structure Analysis of Macrophage Migration Inhibitory Factor in complex with… · 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 4P0H · PDBe 4P0H · UniProt P14174
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