Research workbench
Crystal structure of fkrp in complex with mg ion, zinc low remote data
Analyse Crystal structure of fkrp in complex with mg ion, zinc low remote data in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L7T
- Type
- protein
- Length
- 1,759 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fukutin-related protein
- EC
- 2.4.2.-
- UniProt
- Q9H9S5
- Ligands
- NAG, MG, ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fukutin-related protein (EC 2.4.2.-) | protein | 443 | 31% helix, 27% strand | Q9H9S5 |
| B | Fukutin-related protein (EC 2.4.2.-) | protein | 445 | 29% helix, 26% strand | Q9H9S5 |
| C | Fukutin-related protein (EC 2.4.2.-) | protein | 441 | 31% helix, 27% strand | Q9H9S5 |
| D | Fukutin-related protein (EC 2.4.2.-) | protein | 430 | 30% helix, 27% strand | Q9H9S5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 6 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.78 | 0.85 | 56 | empty |
| 2 | 608 | 0.74 | 0.81 | 44 | empty |
| 3 | 580 | 0.73 | 0.81 | 51 | empty |
| 4 | 614 | 0.73 | 0.80 | 48 | empty |
| 5 | 569 | 0.72 | 0.80 | 52 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1566 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1516 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 828 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 697 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 95 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 6L7T · Crystal structure of FKRP in complex with Mg ion, Zinc low remote data · 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 D against A, TM-score 0.99
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 6L7T · PDBe 6L7T · UniProt Q9H9S5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.