MolNFT v1 · #59979 · protein
Structure of macrophage migration inhibitory factor covalently inhibited by pmsf treatment
3CE4: “Structure of macrophage migration inhibitory factor covalently inhibited by pmsf treatment”. X-ray diffraction, 2 ligands (PMS, SO4), 5 pockets (best druggability 0.83). MolNFT v1 #59979 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3CE4
- 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
- UniProt
- P14174
- Ligands
- PMS, SO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Macrophage migration inhibitory factor (EC 5.3.2.1) | protein | 114 | 39% helix, 31% strand | P14174 |
Ligands and binding sites
- PMS · phenylmethanesulfonic acid · ligand · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains B, C
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B, 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 | 417 | 0.83 | 0.91 | 50 | empty |
| 2 | 56 | 0.54 | 0.88 | 13 | PMS |
| 3 | 54 | 0.52 | 0.87 | 13 | PMS |
| 4 | 52 | 0.52 | 0.87 | 13 | PMS |
| 5 | 109 | 0.36 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1145 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1139 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1136 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 3CE4 · Structure of Macrophage Migration Inhibitory Factor Covalently Inhibited by PMSF Treatment · 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 3CE4 · PDBe 3CE4 · UniProt P14174
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