MolNFT v1 · #140310 · protein
Human serum trnasferrin bound to a fluorescent probe
5Y6K · Serotransferrin: “Human serum trnasferrin bound to a fluorescent probe”. X-ray diffraction, 2 ligands (8R6, FE), 7 pockets (best druggability 0.78). MolNFT v1 #140310 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y6K
- Type
- protein
- Length
- 649 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serotransferrin
- UniProt
- P02787
- Ligands
- 8R6, FE
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serotransferrin | protein | 649 | 36% helix, 19% strand | P02787 |
Ligands and binding sites
- 8R6 · (2S)-6-[2-(7-azido-4-methyl-2-oxidanylidene-chromen-3-yl)ethanoylamino]-2-[bis(2-hydroxy-2-oxoethyl) amino]hexanoic acid · ligand · 2 copies · chains A
- FE · Fe (III) ion · metal · 2 copies · chains A
- MLI · Malonate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.78 | 0.82 | 81 | MLI |
| 2 | 747 | 0.76 | 0.81 | 68 | empty |
| 3 | 179 | 0.59 | 0.82 | 20 | empty |
| 4 | 93 | 0.36 | 0.75 | 22 | empty |
| 5 | 76 | 0.35 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
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 P02787
- Elsewhere: RCSB PDB 5Y6K · PDBe 5Y6K · UniProt P02787
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