Research workbench
Crystal structure of udp-glcnac inverting 4,6-dehydratase in complex with NADPH and udp-glcnac
Analyse Crystal structure of udp-glcnac inverting 4,6-dehydratase in complex with NADPH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GN4
- 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
- NDP, UD1
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glcnac C6 dehydratase (EC 4.2.1.-) | protein | 329 | 37% helix, 20% strand | O25511 |
| B | Udp-glcnac C6 dehydratase (EC 4.2.1.-) | protein | 327 | 37% helix, 22% strand | O25511 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains B, A
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 | 895 | 0.84 | 0.86 | 83 | NDP, UD1 |
| 2 | 930 | 0.84 | 0.85 | 82 | NDP, UD1 |
| 3 | 59 | 0.52 | 0.87 | 20 | empty |
| 4 | 58 | 0.51 | 0.86 | 21 | empty |
| 5 | 87 | 0.34 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1209 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2GN4 · Crystal structure of UDP-GlcNAc inverting 4,6-dehydratase in complex with NADPH and… · the same entry in another collection · chain A against A, 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 0.99
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 2GN4 · PDBe 2GN4 · UniProt O25511
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