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Crystal structure of plasmodium falciparum orotidine 5'-monophosphate decarboxylase complexed with 6-amino-ump
Analyse Crystal structure of plasmodium falciparum orotidine 5'-monophosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N3M
- Type
- protein
- Length
- 650 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- Q8IJH3
- Ligands
- NUP, PO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 328 | 54% helix, 15% strand | Q8IJH3 |
| B | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 322 | 55% helix, 16% strand | Q8IJH3 |
Ligands and binding sites
- NUP · 6-aminouridine 5'-monophosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.76 | 0.96 | 30 | NUP |
| 2 | 108 | 0.76 | 0.96 | 30 | NUP |
| 3 | 125 | 0.45 | 0.77 | 19 | GOL |
| 4 | 130 | 0.43 | 0.76 | 18 | empty |
| 5 | 119 | 0.40 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2515 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3N3M · Crystal structure of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase… · 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 Q8IJH3
- Elsewhere: RCSB PDB 3N3M · PDBe 3N3M · UniProt Q8IJH3
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