MolNFT v1 · #81386 · protein
Crystal structure of otemo complex with FAD and NADP (form 3)
3UP4: “Crystal structure of otemo complex with FAD and NADP (form 3)”. X-ray diffraction, 2 ligands (FAD, NAP), 10 pockets (best druggability 0.84). MolNFT v1 #81386 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3UP4
- Type
- protein
- Length
- 1,061 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Otemo
- EC
- 1.-.-.-
- Ligands
- FAD, NAP
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Otemo (EC 1.-.-.-) | protein | 528 | 35% helix, 19% strand | — |
| B | Otemo (EC 1.-.-.-) | protein | 533 | 34% helix, 20% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.84 | 0.85 | 89 | FAD, NAP |
| 2 | 1016 | 0.84 | 0.85 | 90 | FAD, NAP |
| 3 | 799 | 0.80 | 0.83 | 96 | empty |
| 4 | 148 | 0.61 | 0.84 | 23 | empty |
| 5 | 195 | 0.54 | 0.79 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 1128 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3UP4 · Crystal Structure of OTEMO complex with FAD and NADP (form 3) · 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
- Elsewhere: RCSB PDB 3UP4 · PDBe 3UP4
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