Research workbench
Multiple binding modes of benzyl isothiocyanate inhibitor complexed with macrophage migration inhibitory factor
Analyse Multiple binding modes of benzyl isothiocyanate inhibitor complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WNR
- 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
- 9BE, SO4, CL
- Pockets
- 3 · best druggability 0.81
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, 5.3.3.12) | protein | 114 | 39% helix, 31% strand | P14174 |
Ligands and binding sites
- 9BE · N-benzylthioformamide · ligand · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.81 | 0.86 | 68 | empty |
| 2 | 78 | 0.59 | 0.88 | 13 | 9BE |
| 3 | 53 | 0.43 | 0.83 | 12 | 9BE |
Interfaces
3 interfaces between chains.
- A–C · 1146 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1141 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1140 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 3WNR · Multiple binding modes of benzyl isothiocyanate inhibitor complexed with Macrophage… · 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 3WNR · PDBe 3WNR · UniProt P14174
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