Research workbench
Crystal structure of streptomyces sviceus ssdesb in complex with NADP+
Analyse Crystal structure of streptomyces sviceus ssdesb in complex with NADP+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XBB
- Type
- protein
- Length
- 3,336 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monooxigenase
- UniProt
- B5HNG5
- Ligands
- FAD, NAP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Monooxigenase | protein | 418 | 35% helix, 22% strand | B5HNG5 |
| B, C, F, G | Monooxigenase | protein | 416 | 35% helix, 23% strand | B5HNG5 |
| D, E | Monooxigenase | protein | 417 | 35% helix, 22% strand | B5HNG5 |
| H | Monooxigenase | protein | 420 | 34% helix, 22% strand | B5HNG5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.85 | 0.87 | 89 | FAD, NAP |
| 2 | 891 | 0.84 | 0.86 | 90 | FAD, NAP |
| 3 | 1158 | 0.84 | 0.85 | 112 | FAD, NAP |
| 4 | 833 | 0.84 | 0.86 | 94 | FAD, NAP |
| 5 | 1085 | 0.84 | 0.84 | 95 | FAD, NAP |
Interfaces
15 interfaces between chains.
- B–D · 2131 Ų buried · 28 hydrogen bonds · protein-protein
- F–H · 2107 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 2103 Ų buried · 32 hydrogen bonds · protein-protein
- E–G · 2086 Ų buried · 30 hydrogen bonds · protein-protein
- F–G · 1905 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6XBB · Crystal structure of Streptomyces sviceus SsDesB in complex with NADP+ · 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 B5HNG5
- Elsewhere: RCSB PDB 6XBB · PDBe 6XBB · UniProt B5HNG5
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