Research workbench
Human orotidyl-5'-monophosphate decarboxylase in complex with 5-cyano- ump
Analyse Human orotidyl-5'-monophosphate decarboxylase in complex with 5-cyano- ump in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EWZ
- Type
- protein
- Length
- 1,029 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine-5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- P11172
- Ligands
- CNU, SO4
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Orotidine-5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 258 | 41% helix, 17% strand | P11172 |
| C | Orotidine-5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 257 | 44% helix, 18% strand | P11172 |
| D | Orotidine-5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 256 | 42% helix, 18% strand | P11172 |
Ligands and binding sites
- CNU · 5-cyano-uridine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.86 | 0.88 | 124 | CNU |
| 2 | 139 | 0.76 | 0.94 | 34 | CNU |
| 3 | 170 | 0.72 | 0.90 | 44 | CNU |
| 4 | 124 | 0.70 | 0.91 | 35 | CNU |
| 5 | 77 | 0.35 | 0.76 | 16 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1976 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1940 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 536 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 192 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3EWZ · human orotidyl-5'-monophosphate decarboxylase in complex with 5-cyano-UMP · 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 3EWZ · PDBe 3EWZ · UniProt P11172
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