MolNFT v1 · #48641 · protein
Crystal structure of the bordetella bronchiseptica enzyme wbmg in complex with NAD and udp
2PZL · Putative nucleotide sugar epimerase/ dehydratase: “Crystal structure of the bordetella bronchiseptica enzyme wbmg in complex with NAD and udp”. X-ray diffraction, 2 ligands (NAD, UDP), 3 pockets (best druggability 0.78). MolNFT v1…
- 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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