Research workbench
Apo structure of terb, an NADP dependent oxidoreductase in the terfestatin biosynthesis pathway
Analyse Apo structure of terb, an NADP dependent oxidoreductase in the terfestatin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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