MolNFT v1 · #103566 · protein
Crystal structure of macrophage migration inhibitory factor in complex with furan-2-YLMETHYL)IMINO methanethiol
4PKK: “Crystal structure of macrophage migration inhibitory factor in complex with furan-2-YLMETHYL)IMINO…”. X-ray diffraction, 2 ligands (31E, SO4), 5 pockets (best druggability 0.84). MolNFT v1 #103566 on GenesisL1: 3D structure, binding…
- PDB
- 4PKK
- 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
- Ligands
- 31E, SO4
- Pockets
- 5 · best druggability 0.84
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
- 31E · (Z)-[(furan-2-ylmethyl)imino]methanethiol · ligand · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, C, B
- IPA · Isopropyl alcohol · additive · 4 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.84 | 0.92 | 46 | empty |
| 2 | 92 | 0.56 | 0.85 | 13 | 31E |
| 3 | 89 | 0.53 | 0.83 | 16 | 31E, IPA |
| 4 | 92 | 0.53 | 0.83 | 13 | 31E |
| 5 | 99 | 0.34 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1181 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1149 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1141 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4PKK · Crystal structure of Macrophage Migration inhibitory factor in complex with… · the same entry in another collection · chain B against B, 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 4PKK · PDBe 4PKK · UniProt P14174
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