Research workbench
Crystal structure of udp-glcnac inverting 4,6-dehydratase in complex with NADP and udp-gal
Analyse Crystal structure of udp-glcnac inverting 4,6-dehydratase in complex with NADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GNA
- Type
- protein
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glcnac C6 dehydratase
- EC
- 4.2.1.-
- UniProt
- O25511
- Ligands
- GDU, NAP
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glcnac C6 dehydratase (EC 4.2.1.-) | protein | 329 | 34% helix, 18% strand | O25511 |
| B | Udp-glcnac C6 dehydratase (EC 4.2.1.-) | protein | 327 | 38% helix, 20% strand | O25511 |
Ligands and binding sites
- GDU · Galactose-uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.84 | 0.85 | 72 | GDU, NAP |
| 2 | 1056 | 0.84 | 0.84 | 89 | GDU, NAP |
| 3 | 73 | 0.54 | 0.86 | 19 | empty |
| 4 | 61 | 0.51 | 0.86 | 20 | empty |
| 5 | 78 | 0.47 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1131 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2GNA · Crystal structure of UDP-GlcNAc inverting 4,6-dehydratase in complex with NADP and UDP-Gal · the same entry in another collection · chain B against B, TM-score 1.00
- O25511 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine 4,6-dehydratase (inverting)… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O25511
- Elsewhere: RCSB PDB 2GNA · PDBe 2GNA · UniProt O25511
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