MolNFT v1 · #93955 · protein
Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with cmp-N4-oh
4HIB · Uridine 5'-monophosphate synthase: “Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with cmp-N4-oh”. X-ray diffraction, 2 ligands (16B, CL), 4 pockets (best druggability 0.74). MolNFT v1 #93955 on…
- PDB
- 4HIB
- 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
- 4.1.1.23
- UniProt
- P11172
- Ligands
- 16B, CL
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridine 5'-monophosphate synthase (EC 4.1.1.23) | protein | 256 | 45% helix, 17% strand | P11172 |
Ligands and binding sites
- 16B · N-hydroxycytidine 5'-(dihydrogen phosphate) · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.74 | 0.90 | 41 | 16B |
| 2 | 118 | 0.73 | 0.94 | 31 | 16B |
| 3 | 55 | 0.34 | 0.79 | 17 | empty |
| 4 | 53 | 0.30 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1908 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 4HIB · Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with… · 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 4HIB · PDBe 4HIB · UniProt P11172
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