Research workbench
Crystal structure of a putative 2-deoxy-D-gluconate 3-dehydrogenase from agrobacterium tumefaciens (target efi-506435) with bound NADP
Analyse Crystal structure of a putative 2-deoxy-D-gluconate 3-dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HP8
- Type
- protein
- Length
- 491 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-deoxy-D-gluconate 3-dehydrogenase
- UniProt
- A9CEQ9
- Ligands
- NAP
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-deoxy-D-gluconate 3-dehydrogenase | protein | 245 | 45% helix, 16% strand | A9CEQ9 |
| B | 2-deoxy-D-gluconate 3-dehydrogenase | protein | 246 | 46% helix, 16% strand | A9CEQ9 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.76 | 0.84 | 53 | NAP |
| 2 | 359 | 0.75 | 0.86 | 45 | NAP, ACT |
| 3 | 152 | 0.48 | 0.77 | 20 | empty |
| 4 | 161 | 0.46 | 0.76 | 27 | empty |
| 5 | 96 | 0.35 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1376 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4HP8 · Crystal structure of a putative 2-deoxy-d-gluconate 3-dehydrogenase from Agrobacterium… · 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 A9CEQ9
- Elsewhere: RCSB PDB 4HP8 · PDBe 4HP8 · UniProt A9CEQ9
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