Research workbench
2.9 ångström resolution crystal structure of dtdp-glucose 4,6- dehydratase (rfbb) from bacillus anthracis str. ames in complex with NAD.
Analyse 2.9 ångström resolution crystal structure of dtdp-glucose 4,6- dehydratase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BI4
- Type
- protein
- Length
- 1,242 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dtdp-glucose 4,6-dehydratase
- EC
- 4.2.1.46
- UniProt
- Q81TP0
- Ligands
- NAD, GLC, FRU, NI, SO4
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dtdp-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 311 | 44% helix, 18% strand | Q81TP0 |
| B, D | Dtdp-glucose 4,6-dehydratase (EC 4.2.1.46) | protein | 310 | 44% helix, 18% strand | Q81TP0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, C, B, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, C, B, D
- NI · Nickel (II) ion · metal · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.79 | 0.83 | 65 | NAD, SO4 |
| 2 | 697 | 0.79 | 0.83 | 66 | NAD, SO4 |
| 3 | 718 | 0.78 | 0.83 | 64 | NAD, SO4 |
| 4 | 700 | 0.78 | 0.83 | 66 | NAD, SO4 |
| 5 | 125 | 0.48 | 0.79 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–D · 982 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 969 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 488 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 6BI4 · 2.9 Angstrom Resolution Crystal Structure of dTDP-Glucose 4,6-dehydratase (rfbB) from… · 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 Q81TP0
- Elsewhere: RCSB PDB 6BI4 · PDBe 6BI4 · UniProt Q81TP0
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