Research workbench
Ancylostoma ceylanicum mif in complex with N-(2,3,4,5,6-pentafluoro- benzyl)-4-sulfamoyl-benzamide
Analyse Ancylostoma ceylanicum mif in complex with N-(2,3,4,5,6-pentafluoro… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RF5
- Type
- protein
- Length
- 348 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage migration inhibitory factor
- UniProt
- A4GRE3
- Ligands
- FUZ, ZN
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Macrophage migration inhibitory factor | protein | 116 | 38% helix, 30% strand | A4GRE3 |
Ligands and binding sites
- FUZ · 2-[(furan-2-ylmethyl)amino]benzoic acid · ligand · 3 copies · chains A, C, B
- ZN · Zinc ion · metal · 7 copies · chains A, C, B
- ACT · Acetate ion · additive · 4 copies · chains A, C, B
- IMD · Imidazole · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.79 | 0.98 | 17 | empty |
| 2 | 72 | 0.55 | 0.86 | 17 | FUZ |
| 3 | 76 | 0.53 | 0.85 | 18 | FUZ |
| 4 | 193 | 0.52 | 0.77 | 18 | empty |
| 5 | 75 | 0.51 | 0.84 | 18 | FUZ |
Interfaces
3 interfaces between chains.
- A–C · 1224 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1222 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1208 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3RF5 · Ancylostoma ceylanicum mif in complex with n-(2,3,4,5,6-pentafluoro-benzyl)-4-sulfamoyl-be… · 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 A4GRE3
- Elsewhere: RCSB PDB 3RF5 · PDBe 3RF5 · UniProt A4GRE3
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