Research workbench
Crystal structure of hypothetical dtdp-4-dehydrorhamnose reductase from sulfolobus tokodaii
Analyse Crystal structure of hypothetical dtdp-4-dehydrorhamnose reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GGS
- Type
- protein
- Length
- 546 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 273AA long hypothetical dtdp-4-dehydrorhamnose reductase
- EC
- 1.1.1.133
- UniProt
- Q96Z61
- Ligands
- NDP
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 273AA long hypothetical dtdp-4-dehydrorhamnose reductase (EC 1.1.1.133) | protein | 273 | 40% helix, 18% strand | Q96Z61 |
Ligands and binding sites
- NDP · Nadph dihydro-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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.75 | 0.81 | 51 | NDP |
| 2 | 666 | 0.75 | 0.81 | 55 | NDP |
| 3 | 301 | 0.64 | 0.81 | 33 | empty |
| 4 | 157 | 0.52 | 0.79 | 25 | empty |
| 5 | 147 | 0.47 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 868 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2GGS · crystal structure of hypothetical dTDP-4-dehydrorhamnose reductase from sulfolobus… · 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 Q96Z61
- Elsewhere: RCSB PDB 2GGS · PDBe 2GGS · UniProt Q96Z61
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