Research workbench
Crystal structure of fkrp in complex with mg ion and cmp
Analyse Crystal structure of fkrp in complex with mg ion and cmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KAL
- Type
- protein
- Length
- 1,772 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fukutin-related protein
- UniProt
- Q9H9S5
- Ligands
- C5P, NAG, MG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fukutin-related protein | protein | 443 | 30% helix, 28% strand | Q9H9S5 |
| B | Fukutin-related protein | protein | 445 | 29% helix, 26% strand | Q9H9S5 |
| C | Fukutin-related protein | protein | 441 | 29% helix, 27% strand | Q9H9S5 |
| D | Fukutin-related protein | protein | 443 | 29% helix, 27% strand | Q9H9S5 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc 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
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.83 | 0.84 | 97 | empty |
| 2 | 567 | 0.74 | 0.82 | 48 | empty |
| 3 | 620 | 0.73 | 0.80 | 51 | empty |
| 4 | 713 | 0.73 | 0.79 | 46 | empty |
| 5 | 530 | 0.73 | 0.81 | 52 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1524 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1492 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 840 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 692 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 83 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).
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 Q9H9S5
- Elsewhere: RCSB PDB 6KAL · PDBe 6KAL · UniProt Q9H9S5
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