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Crystal structure of putative glucose 1-dehydrogenase from burkholderia cenocepacia in complex with NADP and a potential reaction product
Analyse Crystal structure of putative glucose 1-dehydrogenase from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V0H
- Type
- protein
- Length
- 1,982 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glucose 1-dehydrogenase
- EC
- 1.1.1.47
- UniProt
- B4E6Z1
- Ligands
- NAP, OUO, CA, NA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H | Putative glucose 1-dehydrogenase (EC 1.1.1.47) | protein | 247 | 49% helix, 15% strand | B4E6Z1 |
| G | Putative glucose 1-dehydrogenase (EC 1.1.1.47) | protein | 253 | 48% helix, 15% strand | B4E6Z1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- OUO · (2R)-2-(hydroxymethyl)pentanedioic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, D, B, C, E, H, F, G
- NA · Sodium ion · metal · 6 copies · chains A, C, B, D, E, G, F, H
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.81 | 0.89 | 71 | NAP, OUO |
| 2 | 407 | 0.78 | 0.87 | 46 | NAP, OUO |
| 3 | 384 | 0.77 | 0.87 | 48 | NAP, OUO |
| 4 | 403 | 0.77 | 0.86 | 46 | NAP, OUO |
| 5 | 418 | 0.77 | 0.86 | 47 | NAP, OUO |
Interfaces
18 interfaces between chains.
- C–D · 1548 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1545 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1538 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1506 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1468 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7V0H · Crystal Structure of Putative glucose 1-dehydrogenase from Burkholderia cenocepacia 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 B4E6Z1
- Elsewhere: RCSB PDB 7V0H · PDBe 7V0H · UniProt B4E6Z1
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