MolNFT v1 · #105311 · protein
Structure of udp-D-mannac dehdrogeanse from pyrococcus horikoshii
4R16 · 418AA long hypothetical udp-N-acetyl-D-mannosaminuronic…: “Structure of udp-D-mannac dehdrogeanse from pyrococcus horikoshii”. X-ray diffraction, 1 ligand (SAJ), 2 pockets (best druggability 0.80). MolNFT v1 #105311 on GenesisL1: 3D…
- PDB
- 4R16
- Type
- protein
- Length
- 836 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 418AA long hypothetical udp-N-acetyl-D-mannosaminuronic acid dehydrogenase
- UniProt
- O59284
- Ligands
- SAJ
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 418AA long hypothetical udp-N-acetyl-D-mannosaminuronic acid dehydrogenase | protein | 418 | 42% helix, 16% strand | O59284 |
Ligands and binding sites
- SAJ · (2S,3S,4R,5S,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,4-bis(oxidanyl)oxane-2-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.80 | 0.82 | 85 | SAJ |
| 2 | 904 | 0.78 | 0.81 | 91 | SAJ |
Interfaces
1 interface between chains.
- A–B · 2822 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4R16 · Structure of UDP-D-MAnNAc dehdrogeanse from Pyrococcus horikoshii · the same entry in another collection · chain A against A, TM-score 1.00
- O59284 · AlphaFold monomer V2.0 prediction for udp-N-acetyl-D-mannosamine dehydrogenase (O59284) · a predicted model of the same protein · chain A 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 O59284
- Elsewhere: RCSB PDB 4R16 · PDBe 4R16 · UniProt O59284
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