MolNFT v1 · #143996 · protein
Crystal structure of G107A mutant of human macrophage migration inhibitory factor
6BG7: “Crystal structure of G107A mutant of human macrophage migration inhibitory factor”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.84). MolNFT v1 #143996 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6BG7
- 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
- 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
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, B
- GOL · Glycerol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.84 | 0.91 | 49 | empty |
| 2 | 52 | 0.54 | 0.88 | 12 | GOL |
| 3 | 77 | 0.48 | 0.82 | 16 | GOL |
| 4 | 71 | 0.46 | 0.81 | 13 | empty |
| 5 | 147 | 0.40 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1197 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1173 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1128 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6BG7 · Crystal structure of G107A mutant of human macrophage migration inhibitory factor · the same entry in another collection · chain C against C, 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 6BG7 · PDBe 6BG7 · UniProt P14174
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