Research workbench
Fv M6P-1 in complex with mannose-6-phosphate
Analyse Fv M6P-1 in complex with mannose-6-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RZC
- Type
- protein
- Length
- 912 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fv M6P-1 light chain; Fv M6P-1 heavy chain
- Ligands
- M6P, SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fv M6P-1 light chain | protein | 118 | 5% helix, 55% strand | — |
| L | Fv M6P-1 heavy chain | protein | 110 | 3% helix, 49% strand | — |
| A | Fv M6P-1 light chain | protein | 119 | 5% helix, 55% strand | — |
| B | Fv M6P-1 heavy chain | protein | 109 | 3% helix, 50% strand | — |
| C, E | Fv M6P-1 light chain | protein | 117 | 5% helix, 56% strand | — |
| D, F | Fv M6P-1 heavy chain | protein | 111 | 3% helix, 49% strand | — |
Ligands and binding sites
- M6P · 6-O-phosphono-alpha-D-mannopyranose · ligand · 4 copies · chains H, L, A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains L, B, D, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.74 | 0.80 | 80 | M6P |
| 2 | 255 | 0.55 | 0.77 | 43 | empty |
| 3 | 66 | 0.48 | 0.84 | 24 | empty |
| 4 | 202 | 0.47 | 0.74 | 22 | empty |
| 5 | 80 | 0.36 | 0.76 | 19 | empty |
Interfaces
12 interfaces between chains.
- H–L · 1015 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 987 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 969 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 951 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 661 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4RZC · Fv M6P-1 in complex with mannose-6-phosphate · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 4RZC · PDBe 4RZC
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