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Crystal structure of the wlba dehydrognase from chromobactrium violaceum in complex with NADH and udp-glcnaca at 1.50 a resolution
Analyse Crystal structure of the wlba dehydrognase from chromobactrium violaceum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q2I
- Type
- protein
- Length
- 345 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehydrogenase
- UniProt
- Q7NQL0
- Ligands
- NAI, HP7, NA, CL
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dehydrogenase | protein | 345 | 38% helix, 25% strand | Q7NQL0 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains A
- HP7 · (2S,3S,4R,5R,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4-dihydroxy-oxane-2-carboxylic acid · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.60 | 0.78 | 40 | NAI, HP7 |
| 2 | 156 | 0.49 | 0.78 | 25 | empty |
| 3 | 63 | 0.29 | 0.73 | 12 | empty |
| 4 | 51 | 0.27 | 0.74 | 12 | empty |
| 5 | 52 | 0.26 | 0.74 | 19 | empty |
Compared structures
- 3Q2I · Crystal structure of the WlbA dehydrognase from Chromobactrium violaceum in complex with… · 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 Q7NQL0
- Elsewhere: RCSB PDB 3Q2I · PDBe 3Q2I · UniProt Q7NQL0
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