MolNFT v1 · #159945 · protein
Wild-type nis synthetase desd bound to AMP and substrate analog cadaverine
6P63 · Siderophore synthetase type C desd: “Wild-type nis synthetase desd bound to AMP and substrate analog cadaverine”. X-ray diffraction, 2 ligands (AMP, MG), 20 pockets (best druggability 0.87). MolNFT v1 #159945 on GenesisL1: 3D…
- PDB
- 6P63
- Type
- protein
- Length
- 2,377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Siderophore synthetase type C desd
- UniProt
- Q9L069
- Ligands
- AMP, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Siderophore synthetase type C desd | protein | 594 | 44% helix, 21% strand | Q9L069 |
| C | Siderophore synthetase type C desd | protein | 595 | 44% helix, 21% strand | Q9L069 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, C, B, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.87 | 0.88 | 125 | AMP, MG, GOL |
| 2 | 1152 | 0.84 | 0.85 | 100 | AMP, MG, GOL |
| 3 | 1176 | 0.84 | 0.85 | 107 | AMP, MG |
| 4 | 1145 | 0.83 | 0.84 | 95 | AMP, MG, GOL |
| 5 | 607 | 0.76 | 0.82 | 41 | GOL |
Interfaces
4 interfaces between chains.
- A–C · 2247 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 2190 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 252 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 10 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6P63 · Wild-type NIS synthetase DesD bound to AMP and substrate analog cadaverine · 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 Q9L069
- Elsewhere: RCSB PDB 6P63 · PDBe 6P63 · UniProt Q9L069
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