MolNFT v1 · #128370 · protein
Nlppya in complex with mannosamine
5NO9 · 25 kda protein elicitor: “Nlppya in complex with mannosamine”. X-ray diffraction, 2 ligands (95Z, MG), 6 pockets (best druggability 0.52). MolNFT v1 #128370 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NO9
- Type
- protein
- Length
- 829 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 25 kda protein elicitor
- UniProt
- Q9SPD4
- Ligands
- 95Z, MG
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 25 kda protein elicitor | protein | 202 | 18% helix, 35% strand | Q9SPD4 |
| B | 25 kda protein elicitor | protein | 212 | 19% helix, 35% strand | Q9SPD4 |
| C | 25 kda protein elicitor | protein | 208 | 18% helix, 35% strand | Q9SPD4 |
| D | 25 kda protein elicitor | protein | 207 | 18% helix, 35% strand | Q9SPD4 |
Ligands and binding sites
- 95Z · 2-amino-2-deoxy-alpha-D-mannopyranose · ligand · chains D
- MG · Magnesium 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
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.52 | 0.78 | 21 | empty |
| 2 | 172 | 0.47 | 0.76 | 22 | empty |
| 3 | 149 | 0.46 | 0.77 | 20 | empty |
| 4 | 111 | 0.45 | 0.78 | 21 | MG, 95Z |
| 5 | 134 | 0.35 | 0.72 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–D · 76 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 62 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5NO9 · NLPPya in complex with mannosamine · the same entry in another collection · 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 Q9SPD4
- Elsewhere: RCSB PDB 5NO9 · PDBe 5NO9 · UniProt Q9SPD4
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