MolNFT v1 · #102226 · protein
Crystal structure of duf (kirre) D1
4OFI · Kin of irre, isoform a: “Crystal structure of duf (kirre) D1”. X-ray diffraction, 2 ligands (NAG, NA), 8 pockets (best druggability 0.72). MolNFT v1 #102226 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4OFI
- Type
- protein
- Length
- 842 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kin of irre, isoform a
- UniProt
- Q9W4T9
- Ligands
- NAG, NA
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, H | Kin of irre, isoform a | protein | 105 | 6% helix, 43% strand | Q9W4T9 |
| C, G | Kin of irre, isoform a | protein | 106 | 3% helix, 42% strand | Q9W4T9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.72 | 0.76 | 78 | empty |
| 2 | 480 | 0.61 | 0.75 | 54 | empty |
| 3 | 467 | 0.59 | 0.74 | 55 | empty |
| 4 | 175 | 0.46 | 0.75 | 21 | empty |
| 5 | 99 | 0.36 | 0.74 | 20 | empty |
Interfaces
12 interfaces between chains.
- E–F · 707 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 702 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 697 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 690 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 221 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4OFI · Crystal Structure of Duf (Kirre) D1 · 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 Q9W4T9
- Elsewhere: RCSB PDB 4OFI · PDBe 4OFI · UniProt Q9W4T9
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