Research workbench
Crystal structure of the bordetella bronchiseptica enzyme wbmg in complex with NAD and udp
Analyse Crystal structure of the bordetella bronchiseptica enzyme wbmg in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PZL
- Type
- protein
- Length
- 619 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative nucleotide sugar epimerase/ dehydratase
- UniProt
- O87988
- Ligands
- NAD, UDP
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative nucleotide sugar epimerase/ dehydratase | protein | 310 | 39% helix, 18% strand | O87988 |
| B | Putative nucleotide sugar epimerase/ dehydratase | protein | 309 | 39% helix, 18% strand | O87988 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.78 | 0.81 | 75 | NAD, UDP |
| 2 | 812 | 0.78 | 0.81 | 71 | NAD, UDP |
| 3 | 396 | 0.62 | 0.77 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 941 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2PZL · Crystal structure of the Bordetella bronchiseptica enzyme WbmG in complex with NAD and UDP · 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 O87988
- Elsewhere: RCSB PDB 2PZL · PDBe 2PZL · UniProt O87988
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