Research workbench
Macrophage migration inhibitory factor (mif) bound to the (R)- stereoisomer of AV1013
Analyse Macrophage migration inhibitory factor (mif) bound to the (R)- stereoisomer of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IJG
- 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
- AVR, CL
- Pockets
- 4 · best druggability 0.84
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
- AVR · (2R)-2-amino-1-[2-(1-methylethyl)pyrazolo[1,5-a]pyridin-3-yl]propan-1-one · ligand · chains B, C
- CL · Chloride ion · ion · 10 copies · chains A, C, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.84 | 0.92 | 45 | empty |
| 2 | 56 | 0.54 | 0.88 | 13 | empty |
| 3 | 50 | 0.52 | 0.88 | 13 | empty |
| 4 | 165 | 0.43 | 0.74 | 19 | CL |
Interfaces
3 interfaces between chains.
- A–C · 1151 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1149 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1112 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3IJG · Macrophage Migration Inhibitory Factor (MIF) Bound to the (R)-Stereoisomer of AV1013 · the same entry in another collection · chain A against A, TM-score 1.00
- P14174 · AlphaFold monomer V2.0 prediction for macrophage migration inhibitory factor (P14174) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 3IJG · PDBe 3IJG · UniProt P14174
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