MolNFT v1 · #103611 · protein
Crystal structure of macrophage migration inhibitory factor in complex with benzaldehyde
4PLU: “Crystal structure of macrophage migration inhibitory factor in complex with benzaldehyde”. X-ray diffraction, 2 ligands (HBX, SO4), 5 pockets (best druggability 0.84). MolNFT v1 #103611 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4PLU
- 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
- HBX, SO4
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 114 | 39% helix, 31% strand | P14174 |
| B | Macrophage migration inhibitory factor (EC 5.3.2.1, 5.3.3.12) | protein | 113 | 35% helix, 31% strand | P14174 |
Ligands and binding sites
- HBX · benzaldehyde · ligand · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.84 | 0.92 | 46 | empty |
| 2 | 66 | 0.49 | 0.84 | 13 | HBX |
| 3 | 62 | 0.47 | 0.84 | 13 | HBX |
| 4 | 59 | 0.47 | 0.84 | 12 | HBX |
| 5 | 156 | 0.44 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1116 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1103 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1079 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4PLU · Crystal structure of Macrophage Migration Inhibitory Factor in complex with benzaldehyde · 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 4PLU · PDBe 4PLU · UniProt P14174
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