MolNFT v1 · #154421 · protein
Crystal structure of fkrp in complex with ba ion, cdp-ribtol, and sugar acceptor
6KAM · Fukutin-related protein: “Crystal structure of fkrp in complex with ba ion, cdp-ribtol, and sugar acceptor”. X-ray diffraction, 8 ligands (CDP, RB0, NAG), 20 pockets (best druggability 0.80). MolNFT v1 #154421 on GenesisL1: 3D…
- PDB
- 6KAM
- Type
- protein
- Length
- 1,779 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fukutin-related protein
- UniProt
- Q9H9S5
- Ligands
- CDP, RB0, NAG, MAN, NGA, ZN, BA, PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fukutin-related protein | protein | 446 | 30% helix, 27% strand | Q9H9S5 |
| B, C | Fukutin-related protein | protein | 445 | 29% helix, 27% strand | Q9H9S5 |
| D | Fukutin-related protein | protein | 443 | 28% helix, 26% strand | Q9H9S5 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- RB0 · D-ribitol · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, A, B, D
- MAN · alpha-D-mannopyranose · sugar · chains D
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- BA · Barium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.80 | 0.85 | 82 | empty |
| 2 | 319 | 0.76 | 0.87 | 42 | CDP, RB0, BA, PO4 |
| 3 | 1156 | 0.75 | 0.78 | 81 | empty |
| 4 | 589 | 0.73 | 0.81 | 50 | empty |
| 5 | 304 | 0.73 | 0.86 | 32 | CDP, RB0, BA |
Interfaces
6 interfaces between chains.
- C–D · 1530 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1483 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 760 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 553 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 52 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 6KAM · Crystal structure of FKRP in complex with Ba ion, CDP-ribtol, and sugar acceptor · the same entry in another collection · chain D against D, TM-score 1.00
- Q9H9S5 · AlphaFold monomer V2.0 prediction for fukutin-related protein (Q9H9S5) · a predicted model of the same protein · 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 Q9H9S5
- Elsewhere: RCSB PDB 6KAM · PDBe 6KAM · UniProt Q9H9S5
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