MolNFT v1 · #145946 · protein
Apo structure of terb, an NADP dependent oxidoreductase in the terfestatin biosynthesis pathway
6D2V · Terb oxidoreductase: “Apo structure of terb, an NADP dependent oxidoreductase in the terfestatin biosynthesis pathway”. X-ray diffraction, 3 ligands (NDP, SCN, CL), 3 pockets (best druggability 0.74). MolNFT v1 #145946 on GenesisL1…
- PDB
- 6D2V
- Type
- protein
- Length
- 621 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terb oxidoreductase
- Ligands
- NDP, SCN, CL
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Terb oxidoreductase | protein | 315 | 39% helix, 19% strand | — |
| B | Terb oxidoreductase | protein | 306 | 38% helix, 21% strand | — |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SCN · Thiocyanate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.74 | 0.81 | 51 | NDP |
| 2 | 631 | 0.74 | 0.80 | 60 | NDP |
| 3 | 57 | 0.40 | 0.81 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1333 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6D2V · Apo Structure of TerB, an NADP Dependent Oxidoreductase in the Terfestatin Biosynthesis… · 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 6D2V · PDBe 6D2V
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