Research workbench
Crystal structure of mannose-6-phosphate reductase from celery (apium graveolens) leaves with NADP+ and mannonic acid bound
Analyse Crystal structure of mannose-6-phosphate reductase from celery (apium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S5F
- Type
- protein
- Length
- 1,236 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Manose-6-phosphate reductase
- UniProt
- A0A1U9WT24
- Ligands
- NAP, CS2
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | Manose-6-phosphate reductase | protein | 309 | 42% helix, 16% strand | A0A1U9WT24 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains B, A, C, D
- CS2 · D-mannonic acid · ligand · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.80 | 0.82 | 105 | NAP, CS2 |
| 2 | 350 | 0.74 | 0.85 | 48 | NAP, CS2 |
| 3 | 418 | 0.72 | 0.83 | 50 | NAP, CS2 |
| 4 | 379 | 0.72 | 0.83 | 50 | NAP, CS2 |
| 5 | 613 | 0.70 | 0.78 | 63 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1669 Ų buried · 23 hydrogen bonds · protein-protein
- B–A · 467 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 285 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7S5F · Crystal structure of mannose-6-phosphate reductase from celery (Apium graveolens) leaves… · 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
- Every structure of UniProt A0A1U9WT24
- Elsewhere: RCSB PDB 7S5F · PDBe 7S5F · UniProt A0A1U9WT24
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