MolNFT v1 · #128357 · protein
Nlppya in complex with glucosamine
5NNW · 25 kda protein elicitor: “Nlppya in complex with glucosamine”. X-ray diffraction, 2 ligands (GCS, MG), 9 pockets (best druggability 0.64). MolNFT v1 #128357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NNW
- Type
- protein
- Length
- 826 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 25 kda protein elicitor
- UniProt
- Q9SPD4
- Ligands
- GCS, MG
- Pockets
- 9 · best druggability 0.64
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 | 210 | 18% helix, 33% strand | Q9SPD4 |
| B | 25 kda protein elicitor | protein | 202 | 18% helix, 37% strand | Q9SPD4 |
| C | 25 kda protein elicitor | protein | 208 | 18% helix, 35% strand | Q9SPD4 |
| D | 25 kda protein elicitor | protein | 206 | 18% helix, 35% strand | Q9SPD4 |
Ligands and binding sites
- GCS · 2-amino-2-deoxy-beta-D-glucopyranose · sugar · 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
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.64 | 0.74 | 85 | empty |
| 2 | 140 | 0.50 | 0.79 | 21 | empty |
| 3 | 119 | 0.45 | 0.78 | 20 | MG |
| 4 | 136 | 0.43 | 0.76 | 20 | empty |
| 5 | 117 | 0.42 | 0.77 | 20 | empty |
Interfaces
6 interfaces between chains.
- B–C · 434 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 433 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 265 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 119 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 111 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5NNW · NLPPya in complex with glucosamine · 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 5NNW · PDBe 5NNW · UniProt Q9SPD4
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