MolNFT v1 · #57849 · protein
X-ray structure of ifabp from human and rat with bound fluorescent fatty acid analogue
3AKM · Fatty acid-binding protein, intestinal: “X-ray structure of ifabp from human and rat with bound fluorescent fatty acid analogue”. X-ray diffraction, 2 ligands (11D, MG), 4 pockets (best druggability 0.89). MolNFT v1 #57849 on…
- PDB
- 3AKM
- Type
- protein
- Length
- 524 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty acid-binding protein, intestinal
- UniProt
- P12104
- Ligands
- 11D, MG
- Pockets
- 4 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fatty acid-binding protein, intestinal | protein | 131 | 11% helix, 59% strand | P12104 |
Ligands and binding sites
- 11D · 11-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino) undecanoic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.89 | 0.92 | 78 | 11D, MG |
| 2 | 363 | 0.83 | 0.92 | 38 | 11D, MG |
| 3 | 385 | 0.83 | 0.91 | 37 | 11D, MG |
| 4 | 987 | 0.70 | 0.74 | 102 | empty |
Interfaces
5 interfaces between chains.
- A–B · 338 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 270 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 221 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 90 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 53 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3AKM · X-ray structure of iFABP from human and rat with bound fluorescent fatty acid analogue · the same entry in another collection · chain D against D, TM-score 1.00
- P12104 · AlphaFold monomer V2.0 prediction for fatty acid-binding protein, intestinal (P12104) · 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 P12104
- Elsewhere: RCSB PDB 3AKM · PDBe 3AKM · UniProt P12104
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