Research workbench
Human ompd-domain of umps in complex with the substrate omp at 1.25 ångströms resolution, 3.55 mgy exposure
Analyse Human ompd-domain of umps in complex with the substrate omp at 1.25 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YVO
- Type
- protein
- Length
- 256 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine 5'-monophosphate synthase
- EC
- 2.4.2.10, 4.1.1.23
- UniProt
- P11172
- Ligands
- OMP, U, SO4
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridine 5'-monophosphate synthase (EC 2.4.2.10, 4.1.1.23) | protein | 256 | 45% helix, 18% strand | P11172 |
Ligands and binding sites
- OMP · Orotidine-5'-monophosphate · ligand · chains A
- U · Uridine-5'-monophosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.52 | 0.79 | 28 | OMP, U |
Modifications
Observed in the structure: 2 modified (acetylation, oxidation).
Compared structures
- 6YVO · Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution… · 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 P11172
- Elsewhere: RCSB PDB 6YVO · PDBe 6YVO · UniProt P11172
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