Research workbench
Crystal structure of NAD-dependent formate dehydrogenase from staphylococcus aureus in complex with NAD
Analyse Crystal structure of NAD-dependent formate dehydrogenase from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TTB
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formate dehydrogenase
- UniProt
- A0A389UHR2
- Ligands
- NAD
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formate dehydrogenase | protein | 331 | 35% helix, 18% strand | A0A389UHR2 |
| B | Formate dehydrogenase | protein | 327 | 35% helix, 19% strand | A0A389UHR2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.68 | 0.82 | 51 | NAD |
| 2 | 340 | 0.58 | 0.76 | 39 | empty |
| 3 | 128 | 0.45 | 0.77 | 26 | empty |
| 4 | 100 | 0.45 | 0.79 | 24 | empty |
| 5 | 67 | 0.32 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2955 Ų buried · 71 hydrogen bonds · protein-protein
Compared structures
- 6TTB · Crystal structure of NAD-dependent formate dehydrogenase from Staphylococcus aureus in… · 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 A0A389UHR2
- Elsewhere: RCSB PDB 6TTB · PDBe 6TTB · UniProt A0A389UHR2
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