Research workbench
Human ompd-domain of umps in complex with substrate omp at 1.10 ångströms resolution, 15 minutes soaking
Analyse Human ompd-domain of umps in complex with substrate omp at 1.10 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OQK
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- 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
- U, OMP, SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridine 5'-monophosphate synthase (EC 2.4.2.10, 4.1.1.23) | protein | 256 | 44% helix, 18% strand | P11172 |
Ligands and binding sites
- U · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
- OMP · Orotidine-5'-monophosphate · ligand · chains A, B
- SO4 · Sulfate ion · ion · 4 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.77 | 0.95 | 32 | OMP, U |
| 2 | 120 | 0.74 | 0.94 | 32 | U |
| 3 | 57 | 0.32 | 0.77 | 18 | empty |
| 4 | 50 | 0.31 | 0.77 | 16 | empty |
| 5 | 52 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1912 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (acetylation, oxidation).
Compared structures
- 7OQK · Human OMPD-domain of UMPS in complex with substrate OMP at 1.10 Angstroms resolution, 15… · 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 7OQK · PDBe 7OQK · UniProt P11172
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