Research workbench
Crystal structure analysis of macrophage migration inhibitory factor in complex with N-[(4-CYANOPHENYL)METHYL]METHANETHIOAMIDE
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
- 4P01
- Type
- protein
- Length
- 342 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
- Ligands
- 1ZW, CL
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 114 | 39% helix, 32% strand | P14174 |
Ligands and binding sites
- 1ZW · N-[(4-cyanophenyl)methyl]methanethioamide · ligand · 2 copies · chains A, C, B
- CL · Chloride ion · ion · 3 copies · chains B, C, A
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.84 | 0.91 | 49 | empty |
| 2 | 56 | 0.46 | 0.84 | 13 | 1ZW, CL |
| 3 | 60 | 0.45 | 0.82 | 13 | 1ZW |
| 4 | 135 | 0.40 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1118 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1081 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1078 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4P01 · 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 4P01 · PDBe 4P01 · UniProt P14174
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