MolNFT v1 · #152525 · protein
Crystal structure of YFIB(L43P) in complex with yfir
6IKK: “Crystal structure of YFIB(L43P) in complex with yfir”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.62). MolNFT v1 #152525 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IKK
- Type
- protein
- Length
- 545 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yfib; Yfir
- UniProt
- Q9I4L6, Q9I4L4
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yfib | protein | 124 | 44% helix, 15% strand | Q9I4L6 |
| B | Yfir | protein | 149 | 32% helix, 25% strand | Q9I4L4 |
| C | Yfib | protein | 125 | 43% helix, 14% strand | Q9I4L6 |
| D | Yfir | protein | 147 | 31% helix, 25% strand | Q9I4L4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.62 | 0.83 | 26 | empty |
| 2 | 208 | 0.60 | 0.81 | 28 | empty |
| 3 | 108 | 0.47 | 0.80 | 20 | empty |
| 4 | 88 | 0.47 | 0.81 | 17 | empty |
| 5 | 145 | 0.40 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1689 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1652 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 648 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6IKK · Crystal structure of YfiB(L43P) in complex with YfiR · 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 Q9I4L6
- Every structure of UniProt Q9I4L4
- Elsewhere: RCSB PDB 6IKK · PDBe 6IKK · UniProt Q9I4L6 · UniProt Q9I4L4
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