MolNFT v1 · #118556 · protein
The structure of monooxygenase KSTA11 in complex with NAD and its substrate
5F5N: “The structure of monooxygenase KSTA11 in complex with NAD and its substrate”. X-ray diffraction, 3 ligands (NAD, 5VD, MG), 7 pockets (best druggability 0.75). MolNFT v1 #118556 on GenesisL1: 3D structure, binding sites and pockets…
- 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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