Research workbench
Human ompd-domain of umps in complex with substrate omp at 1.10 ångströms resolution, 30 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
- 7OQN
- 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, SO4
- Pockets
- 6 · best druggability 0.75
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
- 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.75 | 0.95 | 32 | U |
| 2 | 113 | 0.73 | 0.93 | 32 | U |
| 3 | 54 | 0.35 | 0.79 | 16 | empty |
| 4 | 55 | 0.32 | 0.77 | 16 | empty |
| 5 | 53 | 0.31 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1914 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (acetylation, oxidation).
Compared structures
- 7OQN · Human OMPD-domain of UMPS in complex with substrate OMP at 1.10 Angstroms resolution, 30… · 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 7OQN · PDBe 7OQN · UniProt P11172
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