Research workbench
The structure of monooxygenase KSTA11 in complex with NAD and its substrate
Analyse The structure of monooxygenase KSTA11 in complex with NAD and its substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F5N
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monooxygenase
- UniProt
- A0A023GUL3
- Ligands
- NAD, 5VD, MG
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Monooxygenase | protein | 289 | 46% helix, 19% strand | A0A023GUL3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- 5VD · methyl (1~{R},2~{R},4~{S})-2-methyl-2,4,5,7,10-pentakis(oxidanyl)-6,11-bis(oxidanylidene)-3,4-dihydro-1~{H}-tetracene-1-carboxylate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- GOL · Glycerol · additive · 10 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.75 | 0.80 | 65 | NAD, 5VD, GOL |
| 2 | 721 | 0.75 | 0.80 | 69 | NAD, 5VD, GOL |
| 3 | 58 | 0.39 | 0.81 | 18 | empty |
| 4 | 54 | 0.34 | 0.79 | 14 | empty |
| 5 | 60 | 0.33 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1043 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5F5N · The structure of monooxygenase KstA11 in complex with NAD and its substrate · 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 A0A023GUL3
- Elsewhere: RCSB PDB 5F5N · PDBe 5F5N · UniProt A0A023GUL3
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