MolNFT v1 · #48716 · protein
Crystal structure of the bordetella bronchiseptica enzyme wbmf in complex with NAD+ and udp
2Q1U · Putative nucleotide sugar epimerase/ dehydratase: “Crystal structure of the bordetella bronchiseptica enzyme wbmf in complex with NAD+ and udp”. X-ray diffraction, 2 ligands (NAD, UDP), 3 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 2Q1U
- Type
- protein
- Length
- 671 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative nucleotide sugar epimerase/ dehydratase
- UniProt
- O87989
- Ligands
- NAD, UDP
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative nucleotide sugar epimerase/ dehydratase | protein | 336 | 44% helix, 13% strand | O87989 |
| B | Putative nucleotide sugar epimerase/ dehydratase | protein | 335 | 44% helix, 14% strand | O87989 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.77 | 0.81 | 80 | NAD, UDP, GOL |
| 2 | 776 | 0.77 | 0.81 | 80 | NAD, UDP, GOL |
| 3 | 72 | 0.31 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1507 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2Q1U · Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+ and… · 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 O87989
- Elsewhere: RCSB PDB 2Q1U · PDBe 2Q1U · UniProt O87989
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